CENTURI multi-engineering platform
Project list
Update 18/10/2024
BIOINFORMATICS
Applicant: Antoine de Chevigny
Institute: INMED
Engineer: Léa Chabot & Thomas Vannier
Submission date: 17/05/2022
Summary
Loss of the transcription factor Neurod2, which is normally expressed in cortical excitatory neurons, causes autism. Neurod2 KO mice show specific phenotypes such as altered social behavior, neuronal migration, connectivity and excitability. To investigate responsible cell types and genes, we performed sn-RNAseq of Neurod2 WT vs KO cortices at 3 ages. We seek to work with a bioinformatics expert to perform thorough DE analysis between WT and KO cells and thereby identify cell types and genes altered by Neurod2 germline mutation.
Requested task
We already obtained raw data and performed QC on dissociated cortical nuclei from WT vs KO littermates at P8, P16 and P30. The approach is validated by the fact that the experiment was performed with our scRNAseq expert colleague. The first UMAP integrating WT and KO cells indicates that specific cell types are most affected than others by Neurod2 KO. Now we would like to use advanced methods to perform DE analysis and identify cell types and genes most affected by Neurod2 deficiency over time. Once this project will be done, functional experiments will help validating the implications of specific cell types and genes in disease progression.
Applicant: Pierre-François Lenne
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 01/02/2023
Summary
We aim to combine transcriptomic data with immunostaining of aggregates of embryonic stem cells called gastruloids, that mimic the early development of mammalian embryos. We recently performed scRNA-seq of gastruloids at 4 different time points, which coincide with dramatic changes in gene expression, patterning and morphology. We have done a preliminary analysis of the scRNA-seq data but need to perform a more advanced analysis to relate gene expression to tissue patterns and germ layers identities.
Requested task
- Analyze scRNA-seq of organoids at four time points
- Compute RNA velocity map
- Map data to reference tissue identities
- Integrate datasets from gastruloids and mouse
Keywords: Transcriptomic, Temporal Single-Cell RNAseq, stem cells.
Applicant: Laurent Fasano
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 18/03/2023
Summary
Our objective is to understand how the deletion of the Tshz3 gene affects gene expression in the cerebral cortex. To address this question, we deleted Tshz3 in the cerebral cortex by crossing Tshz3Flox/Flox;Rosa26-STOP-tdTomato mice with Emx1-cre;Tshz3Flox/Flox mice. In the progeny, Emx1-cre-expressing cells also express the tdTomato reporter gene, allowing cell sorting by FACS upstream scRNA-seq experiment. We profiled 13831 control and 12748 Tshz3 mutant tdTomato+ cells of postnatal day 7 cerebral cortex. We now need to go from raw data processing through clustering to differential gene expression.
Requested task
1/ Raw data preprocessing, normalization & dimensionality reduction.
2/ Clustering and cluster annotation assigning cell types to each cluster with a strong focus on deep layer-specific genes (Layer 5 and Layer 6).
3/ Use previously annotated cortical single-cell postnatal datasets such as those published by Di Bella et al., 2021, to assign cell types to each cluster.
4/ Differentially genes expression.
Keywords: Transcriptomic, Single-Cell RNAseq.
Applicant: Julie Tomas
Institute: CIML
Engineer: Thomas Vannier
Submission date: 04/07/2023
Summary
There is an important gender bias in malnutrition. In our mouse model of severe undernutrition, females are more resistant to undernutrition than males. We would therefore like to study differences in microbiota composition between undernourished and normo-nourished groups.
Requested task
We would then like to study the differences in microbiota composition between undernourished and normo-nourished groups in several sites of interest:
cecum, faeces and ileum.
For each site of interest (cecum, faeces, ileum), we would like to compare SAM females vs. SAM males, Ctrl females vs. Ctrl males, SAM females vs. Ctrl females, and SAM males vs. Ctrl males.
For the SAM females vs. SAM males and Ctrl females vs. Ctrl males comparisons, it will be important to go down to the species (or even strain?) level to observe differences, as within the same animal species differences are observed further down the taxonomy.
We would also like to compare diversities.
Keywords: Target metagenomics.
Applicant: Fanny Mann
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 15/10/2024
Summary
Tumor ecosystems are composed of multiple cell types, including malignant and non-malignant (stromal, immune, and neural) cells, which communicate through ligand-receptor interactions. However, our understanding of the complex network of cell-cell interactions, particularly the bi-directional dialogue between neural cells and the tumor, remains incomplete. Our aim is to integrate single-cell RNA sequencing data to construct a ligand-receptor interactome between specific neuronal subtypes and the malignant/non-malignant cells in the tumor microenvironment.
Requested task
- The data will be pre-processed and cell types annotated to identify the cells (cancer cells, fibroblasts, macrophages...) and neurons (PEP, NF) of interest.
- The identification of expressed ligands and receptors will be based on curated lists of known ligand-receptor pairs from databases such as CellPhoneDB, CellChat or the literature.
- The ligand-receptor interactions will be analysed by matching expressed ligands in tumour cells with expressed receptors in neurons (and vice versa). The likelihood of each ligand-receptor interaction will be scored based on gene expression levels.
- The data will be filtered using gene ontology terms such as 'axon guidance' and 'neurite growth' to identify the ligands and receptors functionally involved in tumour innervation.
Applicant: Camille Boutin
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 07/10/2024
Summary
We are studying molecular control of multiciliated cells (MCCs) differentiation. We recently generated a proteome data set at different time point of MCCs differentiation. We would like to compare this proteome to existing transcriptome of MCCs to evaluate how regulatory mechanisms of MCCs differentiation are integrated.
Requested task
We will provide two list of proteins expressed at 16h and 24h of differentiation that we would like to compare to two transcriptomic data set :
- Multicilin dependant transcriptome (ie gene up regulated in MCI-HGR condition or gene down regulated in MCI-HGR + E2F4DCT) (Ma et al., 2014)
- Transcriptome of MEF induced in MCCs (ie to 340 genes that were upregulated 1,5 fold p<0,05 in MEF expressing Multicilin + E2F4VP16) (Kim et al., 2018)
Applicant: Ede Rancz
Institute: INMED
Engineer: Thomas Vannier
Submission date: 25/09/2024
Summary
We have a dataset of 50+ neurons from with 4 distinct morphological class. We recorded 25 physiological parameters and would like to cluster the neurons in an unsupervised manner to see 1. what's the relationship between morphology and physiology; 2. can we define subclusters inside the 4 morphological classes.
Requested task
1. Multivariate analysis of the 25 recorded parameters to check for correlations and select the most distinct parameters for clustering.
2. Unsupervised clustering using the selected parameters.
Finished projects
Applicant: Laurent Kodjabachian & Camille Boutin
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 09/11/2020
In eukaryotes, universal cellular functions are compartmentalized in organelles, such as transcription in the nucleus, energy production in the mitochondrion or glycosylation in the Golgi apparatus. However, specialized organelles may also achieve unique tasks in specific cell types. This is the case of the deuterosome that serves as a platform for massive centriole synthesis in multiciliated cells (MCCs). MCCs harbour myriads of motile cilia, which rest on modified centrioles, and beat synchronously to generate polarized hydrodynamic forces (Boutin & Kodjabachian, Curr Opin Genet Dev, 2019). MCCs are present throughout metazoan evolution and serve functions ranging from locomotion of marine larvae and flatworms, to brain homeostasis, mucociliary clearance of pathogens and transportation of gametes in mammals. The deuterosome, however, is found only in the vertebrate phylum, which begs a fascinating question: What did it take for this organelle to emerge through evolution ? In other words, how many new proteins were necessary and how do they interact with more ancestral components to build up the deuterosome ? Recent studies suggested that deuterosomes are built from ancestral cell-cycle proteins combined to MCC-specific cell-cycle paralogs that evolved only in the vertebrate phylum (Zhao et al., Nat Cell Biol, 2013; Al Jord et al, Science 2017; Revinski et al, Nat Commun, 2018). A major goal of our research is to reveal how many such genes were shaped by evolution to make up the vertebrate deuterosome. To this aim, we wish to conduct a bio-informatic screen to identify potential deuterosome components extracted from available MCC transcriptomes. The rationale will consist in focusing on genes expressed in human, mouse and Xenopus MCCs, which are absent in non-vertebrate genomes.
Keywords: Single-cell RNA sequensing
Applicant: Françoise Muscatelli
Institute: INMED
Engineer: Thomas Vannier
Submission date: 13/12/2019
Oxytocin (OT) is a social neurohormone associated with autism spectrum disorder (ASD). MAGEL2 is a gene mutated in pathologies associated with ASD. Previously we have shown that social behavioral alterations in Magel2 tm1.1Mus KO mice are rescued by an OT-treatment in the first week of life. Such positive effect of an OT treatment has been reported in different genetic rodent models of ASD. However, we do not know how an OT treatment in the first week of life can have a long-term effect. Here using transcriptomics and proteomics analyses of a critical brain structure we aim to reveal the differences of transcripts and protein expression between the mutant and wild-type neonates and adult mice having been treated or not with oxytocin after birth.
Keywords: Proteomics, RNA-seq, autism spectrum disorder
Applicant: Philippe Naquet
Institute: CIML
Engineer: Thomas Vannier
Submission date: 04/02/2020
We have identified and demonstrated the role of the VNN pantetheinase in the control of the extracellular degradation pathway of Coenzyme A. VNN1 is a regulator of metabolic adaptation in tissues exposed to damage. In mouse, VNN1 behaves as a tumor suppressor in part through its ability to inhibit the Warburg effect and restore mitochondrial activity. However, additional tumor-intrinsic or extrinsic mechanisms are probably involved. The goal of this project is to obtain bioinformatics help to screen human and mouse tumor databases, ii) identify VNN1-dependent signatures involved in tumor control and iii) test whether similar mechanisms occur in other types of human tumors.
Keywords: bulk RNA-sequencing, data mining, human tumors
Applicant: Rosanna Dono & Diane Rattier
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 26/08/2020
Summary
Human induced pluripotent stem cells (hiPSCs), considered as in vitro equivalent of the human epiblast, are a powerful model to study mechanisms underlying embryonic germ layer differentiation. We explore the impact of physical cues on hiPSC fate acquisition. By taking advantage of hiPSCs with reduced levels of the morphogen regulator, GLYPICAN4 (GPC4; line namely shGPC4) we have highlighted that differentiation of hiPSCs into Primitive streak (PS) like cells relies on an interplay between hiPSC morphology and perception of morphogens. Briefly, the shGPC4 line show altered ,morphological organization of the hiPSC epithelial sheet as highlighted by the presences of cell patches with abnormal tight junction formation and apical constriction processes. Through our cellular and molecular analyses, we have showed that disruption of the hiPSC epithelia integrity enhances competence of these cells to activate TGF-b signaling and to differentiate into PS. At present, we aim to understand whether epithelial integrity directly regulates gene expression in hiPSCs through RNA-sequencing analyses.
Requested task
In order to understand whether the modification of the epithelium integrity, observed in shGPC4, primes hiPSCs for PS differentiation, we performed a bulk RNA-sequencing analysis of WT, shCTRL and shGPC4 hiPSCs (in triplicate each) at the undifferentiated stage. For this project, we need to analyze the raw data from this sequencing experiment. To this aim, the requested tasks are: 1) Clean the raw data, 2) Map the cleaned data on the human genome to obtain a list of expressed genes in each sample, 3) Compare the different samples to obtain a list of differentially expressed genes: WT/shCTRL, WT/shGPC4 and shCTRL/shGPC4.
Keywords: bulk RNA-sequencing, hiPSCs
Applicant: Julie Tomas
Institute: CIML
Engineer: Thomas Vannier
Submission date: 04/09/2020
Summary
Education of our mucosal immune system in early-life influences adult health and the risk of developing non-communicable diseases. This education strongly relies on mucosal surface colonization by microbiota. Due to introduction of solid food, weaning period and its change of microbiota is critical in this process. Developing therapies in youths suffering from undernutrition is a sanitary priority, but information is still lacking concerning intestinal microbiota and immune system relationship. The goal of this project is to study the microbiota composition during weaning with normal diet but also after severe acute malnutrition starting from the weaning.
Requested task
The samples were sequenced for 16S rRNA sequencing on MiSeq technology (Illumina, Inc, San Diego CA 92121, USA) with the paired-end 300 bases pair protocol according to the 16S Metagenomic Sequencing Library Preparation (Illumina) at the Institute Hospitalo-Universitaire Méditerannée Infection, Marseille.
We request the help of a bioinformaticians for analyzing these metadata in order to analyse the composition of the microbiota and to generate statistical analyses such as PCoA, α-diversity, β-diversity, richness, the Shannon index.
Keywords: Metabarcoding, 16S rRNA, intestinal microbiota, immune system.
Applicant: Pierre Milpied, Sébastion Jaeger, Lionel Spinelli
Institute: CIML
Engineer: Muhammad Asif & Thomas Vannier & Guillaume Gay
Submission date: 12/02/2021
Summary
ShIVA is a software allowing any biologist to apply a correct and validated analytic process that corresponds to current state-of-the art, as defined by single-cell data analysis experts. With this tool, non- experts (biologist researchers or engineers) can load single-cell sequencing data, apply the main quality control steps, execute normalization and dimensionality reduction, perform clustering, identify marker genes, and finally visualize the data interactively to execute supervised and non-supervised scientific analyses.
Requested task
Complete the first version of the software with the remaining features to develop.
Develop a complete and finalized version that will be packaged for large diffusion to the CenTuri and global scientific communities.
Deploy an infrastructure on the CenTuri multi-engineering platform to allow CenTuri community users to easily access the tool. Perform communication on the solution to the CenTuri community and provide training. Depending on informatics resources, deploying a worldwide web-access version of ShIVA could also be considered.
Applicant: Marie-Claire Delfini
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 24/02/2021
To identify key downstream events that mediate ERK-induced cellular transformation, we compared mRNA expression in a model of ERK-induced-neoplasia in chicken embryo, with transcriptional changes obtained in different conditions of unrestrained or inhibited ERK signal in mouse and human. Among the conserved genes positively controlled by ERK signal, one of them encodes a protein which promotes multinucleation by triggering ectopic cell fusion. Our goal is to prove that this protein represents a molecular target of human cancers in which the RAS-ERK pathway is deregulated including melanoma, to restrain cancer aggressiveness by limiting multinucleation and thus aneuploidy/heterogeneity of cancer cells.
The gene (and its product) of interest is poorly expressed in solid adult tissue. We found by immunofluorescence that it is expressed in melanoma cell lines and that its expression depends on ERK signal. To confirm that it is expressed in human melanoma and further characterize the expression profile of melanoma cells expressing it, we would like to analyze available single-Cell RNAseq data from human melanoma. To this aim, the requested tasks are: 1) upload the raw data (from 3 different melanoma patients), 2) make the single cell expression profile and do the clustering, 3) make the cell type identification.
Keywords: bulk RNA-sequencing, data mining, human tumors
Applicant: Camille Boutin & Bianca Habermann
Institute: IBDM
Engineer: Muhammad Asif
Submission date: 18/03/2021
Multiciliated cells (MCCs) are widespread in evolution and serve a large spectrum of physiological functions ranging from locomotion in marine larva to airway protection in humans. Beyond the presence of multiple motile cilia, their basic common feature, MCCs present fundamental morphological variations - like the number of cilia per cell and their spatial organization at the apical surface - depending on the tissue/organ where they reside, which may underlie specific functional adaptations. By comparing the transcriptional profile of MCCs from different tissues within a given animal species and between different species of the evolutionary tree, we want to determine to what extent this profile is identical/variable between these cells and whether it underlines MCC subtype specific functions.
Using single cell transcriptomics data sets that have been recently published, the project aims to
1/ Isolate the transcriptional program of MCCs from different tissues within a given animal species and from different species of the evolutionary tree.
2/ Perform comparative analysis and enrichment analysis of these transcriptional programs.
3/ Evaluate the degree of identity between these transcriptional programs.
Keywords: Single-Cell RNA-seq, Multiciliated cells
Applicant: Micaela Boiero Sanders & Alphée Michelot
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 23/09/2021
Some species can assemble their actin cytoskeleton out of a diversity of actin isoforms. The physiological consequences of using different actin isoforms are poorly known. To study this, we used a simple biological system, composed of a unique actin and a limited set of actin-binding proteins and we switched the endogenous actin gene with heterologous actins. Using budding yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton.
We have to control that the origin of the reorganization of the cytoskeleton is due to the expression of different actins in each strain and not to the differential expression of actin binding proteins. For this reason, we sought for the level of expression of the main actin binding proteins in these cells.
For this, we performed total mRNA sequencing of several yeast strains. The analysis required would be the differential expression of targeted proteins in these cells.
Keywords: Bulk RNA-seq, Actin Binding Proteins, Saccharomyces cerevisiae
Applicant: Mar Benavides
Institute: MIO
Engineer: Thomas Vannier
Submission date: 23/09/2021
Project summary
Marine prokaryotes called “diazotrophs” provide the main source of reactive nitrogen in the ocean, sustaining productivity and CO2 uptake. Climate change is expected to raise temperatures, decrease pH and reduce nutrient availability causing a shift towards organic matter use. We exposed cultures of the diazotroph Crocosphaera to three climate change scenarios and measured their metabolic response, comparing organic matter additions with non-amended controls.
Requested task
The experiment consists of a mixed culture of Trichodesmium and Crocosphaera submitted to 3 different climate change scenarios over 10 days. At each sampling point, 2 samples are retrieved for RNA extractions: time zero (no additions) and time final (+DOM addition incubated 24h). We will have ~30-40 samples sequenced 2x50, NovaSeq 6000. The goal is to look at which metabolic pathways change according to the experimental conditions (temperature+pH and DOM).
We will use a metatranscriptomics analysis to explore 1) which physiological mechanisms are activated to keep the intracellular homeostasis and cope with climate change, and 2) infer up/downregulation of genes that encode certain metabolic pathways (particularly those involved in organic matter processing and coping with stress).
Keywords: Metatranscriptomics, Bulk RNAseq, Crocosphaera
Applicant: Camille Boutin
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 20/06/2022
Summary
Multiciliated cells (MCCs) are presents throughout metazoan evolution and serve various physiological functions. Multiple centriole production is a key step of MCCs differentiation which relies on a poorly understood organelle, the Deuterosome. To further characterize deuterosomes, we developed a protocol to isolate deuterosome and analyzed their composition by mass spectrometry. We thus obtained lists of putative components of deuterosomes. The objective of the project is to compare and classify the data sets obtained for three independent purifications. This represents the final step before publication of our work on the molecular and structural characterisation of the deuterosome.
Requested task
The objective of the project is to compare and classify the data sets obtained for three independent deuterosome purifications.
Applicant: Julie Tomas
Institute: CIML
Engineer: Thomas Vannier
Submission date: 09/12/2022
Summary
Education of our mucosal immune system in early-life influences adult health and the risk of developing non-communicable diseases. This education strongly relies on mucosal surface colonization by microbiota. Due to introduction of solid food, weaning period and its change of microbiota is critical in this process. Developing therapies in youths suffering from undernutrition is a sanitary priority, but information is still lacking concerning intestinal microbiota and immune system relationship. The goal of this project is to study the intestinal microbiota from weaning to later stages and impact of this change on the development of the immune system, in particular Peyer's patches.
Keywords: Metabarcoding, 16S rRNA, intestinal microbiota, immune system, weaning stage.
Applicant: Shruti Pothapragada
Institute: IBDM
Engineer: Thomas Vannier
Submission date: 27/07/2023
Summary
The project focuses on the morphogenesis of the posterior endoderm during gastrulation in the Drosophila embryo. The endoderm undergoes an invagination and a polarized flow towards the dorsal anterior of the embryo. The invagination occurs with the activation of Myosin II, initiated by a transcriptional response under the control of the terminal patterning system. But the genetic determinants required for the symmetry-breaking process remain unknown. The aim of the project is to identify these genes with the hypothesis that certain endodermal genes act dorsally to promote invagination or ventrally to repress it.
Requested task
The data set will include raw data from 4 different genotypes, in triplicates. (4 X 3 = 12)
The following tasks will be required:
• Mapping of the sequence reads to the Drosophila genome
• Read counts of different genes present
• DEGs between 4 mutant conditions
• Gene Ontology and pathway analysis for DEGs
Keywords: Bulk RNA-seq, Drosophila melanogaster, developmental biology.
SOFTWARE & DATABASE MANAGEMENT
Applicant: Arnauld Sergé
Institute: LAI
Engineer: Audrey Comte
Submission date: 24/07/2024
Summary
I have developed an algorithm for single molecule tracking, called multi-target tracing (MTT, Sergé et al. Nature Methods 2008) using Matlab. Meanwhile, other algorithms have been developed, for molecule or cell tracking. Among them, Trackmate has become a reference (Tinevez et al. Methods 2017). It is present in FIJI as a plugin. I contacted the responsible engineer at the image analysis platform of Pasteur Institute. He offered me to add MTT in Trackmate, as an option for detection and/or reconnection.
Requested task
The following steps must be included in the workflow :
- First, try to execute the Matlab code with an API in the Trackmate application
- If that doesn't work, translate part or all of the Matlab code into Java.
Applicant: Shruti Pothapragada
Institute: IBDM
Engineer: Audrey Comte
Submission date: 02/11/2023
Summary
The project focuses on the development of an interactive workflow for bulk-RNAseq analyses of the posterior endoderm during gastrulation in the Drosophila embryo. The project aims to enable biologists to easily reproduce this RNA-seq data analysis and to give them the possibility of modifying the step parameters themselves.
Requested task
The following steps must be included in the workflow:
- Check the quality of the raw reads was assessed using the FastQC toolkit.
- Tream the adapters and low-quality reads with Trimmomatic.
- Align the reads against the reference genome with HiSat2.
- Quantify the gene count with feature count.
- Normalize and do the differential expression using DESeq2.
- Produce a report presenting the result.
- Provide external access to this workflow by hosting it on the multi-engineering platform server.
Finished projects
Applicant: Sophie Brasselet
Institute: Institut Fresnel
Engineer: Masoud A. Sharbaf
The 4POLAR is a fluorescence microscopy imaging method that determines the organization of molecules in a 2D plane of sample. For this to happen, the fluorescence emission from the sample is projected along four different linear polarization angles of light (0, 45, 90 and 135 degree polarization) and an image is recorded for each direction. The orientation at each particular pixel of the image is then reported with three angles that indicate planar orientation, wobbling and off plane orientation. The goal of this project is to develop the 4POLAR method as a plugin for the ImageJ (Fiji) platform.
Keywords: 4POLAR imaging, ImageJ, Fiji
Applicant: Hervé Rigneault
Institute: Institut Fresnel
Engineer: Guillaume Gay
Project summary
In the framework of the Centuri Tech Transfer, the mosaic group at the Fresnel Institute develops a multiphoton endoscope platform for 2photon deep brain imaging and coherent Raman label free tissue imaging. The project has received financial support from Centuri in the first Tech Transfer call.
Requested task
The Python software needs some attention to increase its robustness, to improve its calibration auto-process and to deploy new features.
Applicant: CENTURI community
Institute: CENTURI multi-engineering platform
Engineer: Guillaume Gay
Submission date: 20/04/2020
Summary
Data preservation and sharing, beyond publication, is a common issue for the labs of the CENTURI
community.
In this project, we will setup and compare two software solution adapted for the storage and
publication of microscopy data,
- OMERO : https://www.openmicroscopy.org/omero/institution/
- CYTOMINE https://cytomine.be/
Requested task
- Setup both database servers
- Retrieve data from a former omero installation at IBDM
- Retrieve example data from the various labs of CENTURI
- Redact a comparison between the two solutions
- Plan and dimensioning of a future campus-wide platform
Applicant: CENTURI community
Institute: CENTURI multi-engineering platform
Engineer: Guillaume Gay
Submission date: 20/04/2020
Summary
Assessing microscope quality over time ideally requires a regular evaluation of the optical quality through a dedicated characterization protocols, for example PSF characterization with fluorescent beads, or illumination homogeneity for wide field microscope. Unfortunately, such protocols are time consuming and not adapted to current microscopy platform, where a single engineer or technician must maintain many microscopes.
In this project, we explore the direct use of the images produced by the platform users to automatically assess instrument quality over time.
Requested Task
To achieve this, we implement various blind measure algorithm and setup a workflow that :
1. systematically apply those algorithms to all the images in a collection
2. display the measure for each instrument over time on a dashboard
The project should be mainly database agnostic (meaning that it should work with minimal effort for e.g. omero and cytomine).
Applicant: Pierre Henri Puech
Institute: LAI
Engineer: Guillaume Gay
Submission date: 17/06/2020
Code and GUI to analyze and classify Atomic Force Microscopy data
Requested task
Shaping up of the code base, debugging, setting up of Continuous Integration
Applicant: Denis Puthier
Institute: TAGC
Engineer: Guillaume Gay
Submission date: 05/11/2020
Summary
|
Since several years, we have been developing a Python library (Python GTF Toolkit, pygtftk) for the manipulation of genomic coordinates in GTF format. The library can be used in a Python interpreter or via a CLI which exposes more than 50 tools [1]. Among these we have recently developed OLOGRAM (OverLap Of Genomic Regions Analysis using Monte Carlo) and OLOGRAM-MODL (MultipleOverlap combinations with Dictionary Learning) which allow to compute intersection statistics on genomic region datasets using a negative binomial model [2,3]. 1: Lopez F, Charbonnier G, Kermezli Y, Belhocine M, Ferré Q, Zweig N, Aribi M, 2: Ferré Q, Charbonnier G, Sadouni N, Lopez F, Kermezli Y, Spicuglia S, Capponi 3: Ferré Q, Capponi C, Puthier D. Monte Carlo based mining of enriched |
Requested task
The objective is to develop a web interface that would allow:
- The submission of jobs on a scheduler (e.g. slurm)
- The follow-up of the user jobs
As the whole project is written in Python (with some C/C++ and Cython) we believe that it would be meaningful to develop it using a framework like Django. However as we are not expert in web developement we are highly open to suggestion.
We also think that it could be interesting to package the solution so that an OLOGRAM-Web service would be easy to install.
We will elaborate a more advance specification in the near future
Applicant: Sébastien Mailfert
Institute: CIML
Engineer: Guillaume Gay
Submission date: 01/02/2021
Project summary
L'outil de gestion et de suivi de tickets mis en place par Guillaume dans Centuri nous intéresse au CIML
Nous cherchons un outil simple d'utilisation permettant le suivi de nos tickets (pannes, demandes diverses, formations).
Requested task
L'outil développé par Guillaume peut être utilisé par l'ensemble des plateformes du CIML, moyennant quelques modifications.
Nous aimerions avoir une page d'entrée où ensuite chaque plateforme se connecterait à sa propre page.
Nous fourniront un canevas le plus commun à tous les services pour que ça demande le moins de développement possible.
Notre service informatique fournira les ressources nécessaire pour le déploiement au CIML.
Applicant: Pierre-Pascal Lenck-Santini
Institute: INMED
Engineer: Guillaume Gay
Submission date: 23/03/2021
Project summary
The goal is to develop a small application (python or matlab) to interact with another, open-source application software that records electrophysiological data. The electrophysiology interface (open-ephys) is sending out messages via tcp server-client protocol and we need to read these messages to activate, if required a National instrument DAQ board that will send analog signals to a series of optical devices.
Requested task
Help me find the most appropriate strategy to read the tcp messages (matlab, python etc?) write codes that interact with tcp protocols. Write the code with me and, eventually publish it on github.
Applicant: Paul Villoutreix
Institute: LIS
Engineer: Guillaume Gay
Submission date: 14/09/2021
Project summary
Random walks on networks are widely used as a model for dynamics in complex systems at various scales, from molecules, to certain cells in tissues such as T-cells in the lymph node, to agents in a city. Here we present an analytical framework that leads to numerical approximations of the dynamic of a random walk on any large network at any time scale. This method enables us to visualize and characterize the role of local variation in the network structure. In addition, we propose an interactive data visualization platform to follow the dynamics of diffusion from any starting point.
Requested task
We have an interactive visualization platform implemented in Dash that we would like to turn into a fast web app installed on a server.
IMAGE DATA PROCESSING
Applicant: Sham Tlili
Institute: IBDM
Engineer: Mai Hoang
Submission date: 29/06/2024
Project summary
Identifying dynamic events such as a cellular division can be challenging in 4D timelapses of developing tissues such as organoids or embryos. Especially, visualizing and annotating such events in dense 3D stacks obtained by light-sheet microscopy or two-photon microscopy where nuclei are almost in contact is challenging.
I have recently developed an annotation pipeline to annotate cell divisions in the context of a project using CNN to detect divisions automatically from live movies of developing embryonic organoids.
With this visualization method, the tissue section can be "augmented" in 3D by visualizing the surrounding tissue layers in different colors.
Until now, I have used the method using homemade macros in fiji or matlab. However, I would like to use direclty this method in an interactive way (such as enabling to change in live parameters such as colormaps, depth of the local max or average projection).
For that, I would like to have a small NAPARI plugin that enables to do such visualization live and use the label annotations directly on NAPARI.
Requested task
The NAPARI plugin should enable to:
(1) open a large 4D Tiff file
(2) to chose parameters of depth augmentation (the information of how many zslices I want to visualize in parallel
(3) chose the number of colors that i want to use (by default, RGB with G the central plane i and R an average or max projection of n planes above the central plan (planes i-n:i-1) and B an average or max projection of m planes below the central plan (planes i+1:i+m)
(4) having the possibility to change the colormap easily
(5) having options between avergage, max projection in the visualization.
Applicant: Laurent Limozin
Institute: LAI
Engineer: Mai Hoang & Thang LE
Submission date: 11/07/2024
Project summary
Celldetective [1] is an original full GUI python based software developed to analyse
microscopy data of immunological systems studied in LAI and CINAM. It
entails pre-processing, segmentation, tracking, signal analysis based on
classical or deep-learning approaches. It offers new AI model training
capacity for some of these tasks. We believe that the conception and
power of the software entails potential for further applications in the
host labs as well as a broader interest of the Centuri community and beyond.
The software is open source [2] and was developed during the thesis of
Rémy TORRO (Centuri PhD LAI/CINAM). Both LAI and CINAM users will
continue its use and may plan further developments. However the time of
skilled manpower will be lacking in those Institutes.
The support of the MEP is requested to provide all the chances of
further exploitation and development of this project.
References:
[1] https://www.biorxiv.org/content/10.1101/2024.03.15.585250v1
[2] https://github.com/remyeltorro/celldetective
Requested task
The requested task will consist in support and maintenance for a starting duration of 1 year:
- assistance for LAI and CINAM users as well as external users
- address bug reports or install issues
- advertisement with the Centuri community when relevant
Significant feature request or development would be subject to a specific request. A new assessment of the project will be realized in one year.
The engineer will operate via the github issue platform with full developer rights.
He/she will receive an advanced training by the conceptor Rémy Torro over July 2024.
The software will still be hosted on github repository owned by Rémy Torro or Limozin/Sengupta PIs.
Applicant: Sham Tlili
Institute: IBDM
Engineer: Thang LE
Submission date: 26/06/2024
Project summary
Cell aggregates pipette or microfluidic aspirations are valuable tools to quantify cell spheroids, embryonic explants or organoids mechanical properties. For that, the segmentation of these tissues before, during and after aspiration is necessary to precisely measure their dynamic response to the externally applied pressure.
The images in this project are obtained from brightfield/phase contrast images coming from live timelapses of embryonic organoides pipette aspirations. Segmenting precisely the tissue displays some challenges due the variability of contrasts in the image, and the difficulty to identify and separate the tissues from the pipette itself.
Classical segmention strategies such as thresholding are not working in these cases. Moreover, it is important to have a low measurement error as getting precisely the edges of the tissues is key to measure its rapid dynamic response.
Requested task
What would be needed in this project is to:
(1) have a tissue segmentation pipeline robust to sample to sample variation (age /texture of the aspired organoids )
(2) be able to segment the organoid and its aspired part in the pipette over the time
(3) have an automated and user friendly pipeling that enables to process batches of experiments
(4) having an analysis pipeline that can be easily adapted to new data with reasonable variations in imaging conditions
Applicant: Emmanuèle Helfer
Institute: CINaM
Engineer: Mai Hoang
Submission date: 28/06/2024
Project summary
The scientific project aims to elucidate the role of cellular components such as chromatin, nuclear lamina, and the cytoskeleton in determining the rheological properties of cells. To achieve this, cells are subjected to alterations induced by genetic mutations or biochemical treatments and forced through narrow constrictions. The dynamics of cell entry and passage through parallel constrictions is acquired in bright field microscopy at high frame rate (500-1000 fps). The videos are analyzed to capture the cell contour over time and measure the length of the cell tongue entering the constriction.
Currently, raw images are cropped to focus on one or several cells entering the constrictions. These cropped images are manually cleaned to remove interference from neighboring cells, followed by image thresholding and binarization using ImageJ to detect cell contours. This manual cleaning is time-consuming and labor-intensive.
Requested task
| The project aims to implement machine learning for automatic segmentation and tracking of cells, using existing datasets of cropped images and their masks for training. This automated system will enhance efficiency and accuracy in analyzing the cell contour, thus in extracting the rheological properties of cells. It will eliminate the need for manual image cleaning and improve overall data processing. |
Applicant: Yulia Fok
Institute: DyNaMo
Engineer: Thang LE
Submission date: 20/02/2024
Project summary
Biological membranes, made up of lipid bilayers, play an essential role in many biological and chemical processes. Supported lipid bilayers are widely used as biomimetic models for studying them. They can be characterised by atomic force microscopy. This technique uses a fine tip to scan the surface of the sample and determine its topography. This enables the thickness of the lipid bilayer to be measured very precisely, on a nanometric scale. However, to avoid acquisition artefacts, the data must be pre-processed to allow thickness measurements. In particular, the angle between the probe and the surface during scanning induces a tilt in the image, which needs to be levelled. Most processing softwares offer algorithms for doing this, but this step can be really tricky, as the corrections can induce distortions. As lipid bilayers are very thin (few nanometers), any deviation is problematic.
Requested task
| The aim is therefore to develop a data processing routine that allows accurate, reproducible and automatable measurement of the thickness of the lidipid layers at each point in order to process a large number of images. |
Applicant: Sophie Chauvet
Institute: IBDM
Engineer: Thang LE
Submission date: 19/04/2023
Project summary
The team " Neural plasticity in cancer development" at IBDM, studies how neuronal plasticity and function regulate cancer progression in mouse models of pancreatic ductal adenocarcinoma (PDAC). We discovered that axons from different components of the peripheral nervous system innervate precancerous lesions and invasive cancers. We are also exploring how peripheral nerves may lead to accelerated or reduced tumor progression depending on their neurochemical properties.
Requested task
Given the multi-faceted role of the different components of the peripheral nervous system in modulating PDAC progression, neuronal fibers represent an attractive target to curb tumor development and progression. We are currently developing new approaches to target axonal remodeling and neuronal secretion. We are using 3D light sheet fluorescence microscopy to visualize in whole pancreas the architecture of neural networks, their interactions with the tumoral microenvironment and tumor progression. However, manual analysis of 3D images is a tedious and time-consuming task and quality of the analysed data can be low. The main goal of the project is to develop deep learning-based auto-segmentation to automatically segment volumetric images of pancreats to take into account, asymptomatic, metaplasic/neoplasic, tumor tissues and quantify cancer growth and effects of treatments.
Finished projects
Applicant: Alexis Moreau
Institute: CINaM
Engineer: Benoit Dehapiot
Submission date: 08/11/2019
The scientific project is to understand the mechanisms of red blood cell passage through the interendothelial slits of the spleen. Red blood cells pass a physical fitness test through these submicron wide slits and undergo extreme deformations. The objective is to answer the following questions. What are the rheological properties of red blood cells required to pass this test and what are the deformation mechanisms? Are mechanotransduction mechanisms involved, in particular by cascading activation of ion channels (including PIEZO1) leading to a reduction in red blood cell volume? We have developed an in-vitro micro-nanofluidic system that reconstructs slits of physiological dimensions and we are conducting quantitative in-vitro experiments. We observed large populations of red blood cells flowing in these devices and want to extract quantitative data.
To this end, we need to develop an image processing program to recognize the contour and position of individual red blood cells on videos
Keywords: Live segmentation and tracking
Applicant: Lucie Pepino
Institute: IBDM
Engineer: Benoit Dehapiot
Submission date: 03/02/2020
Pain research has been carried on male rodents for decades. Yet, several studies showed that women and men experience pain differently. The use of female subjects to understand the mechanisms explaining sex differences in pain neurobiology is of high interest. A complex network of excitatory and inhibitory interneurons allows the spinal cord to modulate pain by controlling peripheral inputs and spinal cord projection neurons outputs. Few studies investigate sexual differences in the modulation of pain at the spinal cord level.
One part of my project aims at determining whether males and females activate the same spinal neural network following a painful stimulus. I used a double in situ hybridization strategy, on male and female spinal cord sections at 5, 15 and 45 minutes after painful stimulation (n=3 per sex per time-point). I used cFos probe as a read-out for neuronal activity, in combination with specific probes for 6 spinal interneuron subsets identified as responsive to a specific painful stimulation. To this aim, we wish to develop an automatized pipeline allowing: 1) cell nuclei identification 2) positive cells selection 3) positive cells number and fluorescence intensity 4) positive cells localization within the spinal cord 5) males versus females data statistic analysis.
Keywords : Nuclei segmentation
Applicant: Claudio Collinet
Institute: IBDM
Engineer: Benoit Dehapiot
Submission date: 26/06/2020
Project summary :
Pulsed contractions drive many cell and tissue shape changes during animal morphogenesis. In the Drosophila posterior endoderm a polarized cell- and tissue-level wave of Rho1/MyoII activation and cell invagination drives the invagination and its associated anterior movement. MyoII activation in each cell occurs with a characteristic sequence. First, cells spread onto the vitelline membrane and MyoII speckles appear at low levels apically (pre-activation). Then, discrete steps of MyoII activation at high levels occur from the posterior to anterior of cells as they detach from the vitelline membrane.
Requested task :
In order to characterize quantitatively this process we wish to develop an image analysis framework to semi-automatically detect MyoII steps of activation in segmented cells and quantitate their features (intensity, duration, association with actin cortex deformation, position in the cell, etc.). The analysis framework will have to interface with another framework developed in the lab to quantify local MyoII rates of change, cortex advection and MyoII activation reaction kinetics.
Applicant: Dina Aggad
Institute: CIML
Engineer: Benoit Dehapiot
Submission date: 20/10/2020
Project summary :
In order to address how C. elegans cuticular integrity can be sense and translated into transcriptional responses in the epidermis, we turn our attention to a specific structure found at the interface between the cuticle and the epidermis. In addition to its very limited characterization, its function remains unknown. We have described their 2D and 3D structures by electron microscopy and tomography. Using a marker of these organelles, we want to characterize this structure in different mutant conditions.
Requested task :
We would like an automatic pipeline to automatically segment and quantify these organelles in different mutant conditions. From a dataset of confocal fluorescent images, the Fiji macro will include, treatment of different manually selected ROI, definition of specific threshold on two different signals and segmentation of images.
Applicant: Jean-Bernard Manent
Institute: INMED
Engineer: Qingzong Tseng
Submission date: 29/09/2020
Project summary :
During brain development, defective positioning can result in the accumulation of masses (or heterotopia) composed of ectopic neurons, causing epilepsy and intellectual disability. The peculiar morpho-functional characteristics and molecular identity of ectopic neurons however remains poorly understood. In this project, we aim at extracting various morphological features from 3D reconstructed neurons belonging to distinct heterotopia subtypes, or located at distinct spatial location within a given heterotopia subtype. By computing their morphometric statistics, and combining these parameters with their functional features (these neurons have been characterized with electrophysiological methods beforehand), we aim at better characterizing the unique signatures of ectopic neurons.
Requested task :
We wish to utilize MorphoPy, an open source Python package enabling computation of various morphometric statistics and creation of density maps from 3D reconstructed neurons in the standardized -swc format. Prior to running the analysis, we wish to register their proper orientation and position relative to a common landmark, or to the anatomical border of the heterotopia in order to reliably compare morphometric properties. Last, we wish to generate summary plots (and individual plots) for all neurons and subgroups, for visualizing the topographic organization of distinct neuronal compartments (axons, dendrites...) with respect to a common landmark or to the heterotopia.
Applicant: Serge van de Pavert
Institute: CIML
Engineer: Qinzong Tseng
Submission date: 20/05/2020
Lymph nodes are the cross roads of our immune system, connecting the innate and adaptive immunity. They orchestrate effective responses to pathogens and host peripheral tolerance control. Secondary lymphoid organs form during embryonic development in a specific period on specific locations. In this project, we study the role of the neurons in the initiation of embryonic LN formation.
Keywords : LTi, ILC, neuron, lymph node, embryo
Applicant: Elisa Eme-Scolan & Réjane Rua
Institute: CIML
Engineer: Benoit Dehapiot
Submission date: 03/06/2021
Project summary
This project aim to quantify the coverage of blood vessels by perivascular macrophages, depending on the diameter of those vessels. To do so, we wish to use a FIJI macro, to run on maximum intensity projections of confocal images.
Requested task
The services needed are the design of a FIJI macro allowing to quantify the number of macrophages around blood vessels depending on their diameter. The input data will be maximum intensity projections of confocal images, and the output will ideally be a density of cells for several diameters of vessels.
Applicant: Qiyan Mao & Frank Schnorrer
Institute: IBDM
Engineer: Benoit Dehapiot
Submission date: 20/03/2020
Project summary
During skeletal muscle development, hundreds of micrometre-long sarcomeres assemble simultaneously into millimetre-long myofibrils. How are correct numbers of sarcomeres determined? Our previous work in Drosophila indirect flight muscle indicates tension as a mechanical compass to coordinate simultaneous sarcomere self-organisation across the entire length of the myofibril. In this study, we investigate whether the tension-driven myofibril self-organisation mechanism is fundamentally conserved in human myofibers.
We have obtained high resolution immunofluorescence images for overall cultures and individual myofibers during the first two weeks of differentiation. We aim to characterize overall myofiber differentiation by systematically quantifying fiber length, width, fusion index as well as axial coordination between different myofibers. We will further characterize individual myofibers by analyzing sarcomere periodicity. This will offer us crucial inputs to undersand whether myofibrillogenesis takes place simultaneously or sequentially in hiPSC-derived skeletal myofibers. Finally, we have successfully ablated sarcomeric TTN-GFP myofibrils with a femtosecond pulsed IR laser (in collaboration with the Lenne lab). Our preliminary results show clear recoils of myofibril free ends, demonstrating presence of tension. We wish to quantify the recoil of myofibrils post ablation by kymograph analysis.
Keywords : Sarcomere spatial frequency analysis
Applicant: Lucie Boulgakoff and Rachel Sturny
Institute: IBDM
Engineer: Qingzong Tseng
Submission date: 12/11/2020
Project summary
During the first week of life, the mice heart is able to regenerate from a myocardial infarction - this regeneration is made possible by the simultaneous action of multiple processes. Two projects in the lab aim at studying two of these aspects, namely the coronary arteries remodeling and the proliferation of preexisting cardiomyocytes that repopulate the infarcted area. To study these phenomena, we imaged whole cleared hearts with the lightsheet microscope, following a neonatal infarction. Using Cx40-GFP mice line, we aimed at tracking the fluorescent coronary arteries in 3D in order to identify collaterals that appear after infarction and allow the blood to bypass the ligation. In the second project, we genetically labeled cells from the trabecular layer of the heart and aim at quantifying their participation to the repopulation of the infarcted area.
Requested task :
In both of these projects, the postnatal harvested hearts are difficult to image due to their size (around 1cm of diameter) and their opacity. Thus, tiles views and multiangle views of these organs have been acquired with the lightsheet microscope in order to cover the whole sample.
To visualize the totality of the coronary tree in one case, and of the trabecular derivatives in the other one, we would need to fuse the different views in a unique file. For this aim, the requested task consists in 1/ stitching the tile views to obtain one image per angle view 2/ fuse the multiangle views to obtain one single file, in which the Z resolution will be increased by the contribution of different angles. We believe that this method will be useful in the future for other projects beyond our own team.
Applicant: Paul Villoutreix
Institute: LIS
Engineer: Qingzong Tseng
Submission date: 12/10/2020
Project summary
ML is an application of artificial intelligence (AI) that is based on the idea that systems can learn from data, identify patterns and make decisions with minimal human intervention. ML methodologies may therefore uncover hidden data. At this moment, no fully automated method exists to analyze human embryos. Conventional embryo grading after In Vitro Fertilization (IVF) is a subjective evaluation, based on the assessment of morphological characteristics. Previous work has recently been published showing the relevance of using a deep learning method for assessing the quality of blastocyst 110h post insemination (hpi) (Khosravi et al., 2019). Using data from the Leuven University Fertility Center (LUFC), we would like to assess the performance of deep learning models for automatic morphological scoring of fertilized oocytes at earlier stages.
Requested task :
The requested task consists in exploring various deep learning architectures for automatic assessment of fertilized oocytes from a large database of images.
Applicant: Pierre-Henri Puech
Institute: LAI
Engineer: Qingzong Tseng
Submission date: 25/09/2020
Project summary
In the frame of an interdisciplinary project between CINAM (K. Sengupta) and LAI (PH Puech) around mechanotransduction of T cells using traction force microscopy (TFM) supported through a Doc2AMU PhD grant (F. Mustapha, 2nd year).
Requested task :
Help us in adapting our experimental parameters to our small and reactive cells, in finding the right parameters for particle image velocimetry and force maps reconstruction, in determining the resolution in our experiments and guide us through the potential errors and artifacts we may observe.
Applicant: Camille Boutin
Institute: IBDM
Engineer: Qinzong Tseng
Submission date: 25/02/2020
Project summary
To study different aspects of multiciliated cells biology, we apply drug on Xenopus embryos. In these kind of experiments we analyze the fate specification of epidermal cells by double fluorescent in-situ hybridization. I would like to develop an automated pipeline to analyze my confocal acquisitions that would recognize all nuclei of the epidermis and analyze for each nuclei their status (positive/negative) for different cell type markers.
Keywords : Nuclei segmentation
Project cancelled - 01/03/2021
Applicant: Nadine Bruneau
Institute: INMED
Engineer: Benoit Dehapiot
Submission date: 11/05/2021
Project summary :
Reelin is a secreted and signaling glycoprotein serving multiple functions in the brain throughout life which has also emerged as a psychiatric risk factor in a wide spectrum of psychiatric disorders. Reelin critically contributes to early brain development and is also an important contributor to the maturation of functional cortical circuits in the postnatal brain and physiology of the adult central nervous system. Our goal is to address the molecular identity and anatomical organization of reelin neurons during postnatal maturation of the cortex.
Requested task :
We would like a pipeline to automatically count and quantify cells identified by one of two markers by clicking on the image, and cells identification will be confirmed by the presence nucleus. From a dataset of confocal fluorescent images, the Fiji macro will include treatment of different manually selected ROI, definition of specific threshold on two different signals and segmentation of images. Other parameters, such as pixel intensity, area and/or diameter, will be saved in an Excel file before a new run.
Applicant: Camille Laberthonnière, Magdinier Frederique et Anaïs Baudot
Institute: MMG
Engineer: Benoit Dehapiot
Submission date: 21/05/2021
Project summary
To gain further insights into the specificity of the muscle alteration in Facio Scapulo Humeral Dystrophy (FSHD) we derived induced pluripotent stem cells (hiPSCs) from patients and differentiated these cells into contractile innervated muscle fibers. We analyzed their transcriptome by RNA Seq in comparison to cells derived from healthy donors. In FSHD, the vast majority of active modules retrieved with MOGAMUN algorithm converge towards a decreased expression of genes encoding proteins involved in sarcomere organization, Actin cytoskeleton, myofibril, Actin-Myosin sliding and calcium handling.
Requested task
We performed calcium transient analysis using fluorescent Ca2+ indicator and live imaging microscopy to validate the transcriptomic results. From these images, we wanted to extract different parameters such as frequency, amplitude and speed of calcium entry and exit in control and in different patients hiPSCs-derived muscle cells.
Project cancelled - 01/07/2021
Applicant: Nathalie Pujol
Institute: CIML
Engineer: Qingzong Tseng
Submission date: 19/10/2020
Project summary
We are characterizing an unknown organelle in the epidermis of the worm C. elegans by light and electron microscopy. The ultrastructural imaging revealed a membrane-stack organization of the organelle which empedes manual segmentation of 3D datasets. We used two electron microscopy approaches : electron tomography to resolve the 3D structure of these organelles (small volume, high resolution) and serial block face imaging to assess their tissue-level density (high volume, low resolution).
Requested task
In both cases, attempts of semi-automated membrane segmentation were made with relative success, we need an improvement of the segmentation.
We hope that the developments made will by applicable to a broader range of datasets.
Project cancelled
Applicant: Fidan Sumbul
Institute: LAI
Engineer: Thomas Boudier
Submission date: 30/09/2021
Summary
Following the release of the first genome sequence of SARS-CoV-2 virus, many structures have been deposited to the databases including the structure of the ectodomain of Spike protein, stabilized in the prefusion state. While a large amount of structural information of the Spike protein is available, revealing different conformational states, little is known about the dynamics of these conformational changes. In this work, we have used high-speed atomic force microscopy (HS-AFM) with high resolution, to image the ectodomain of S-protein allowing us to visualize the dynamics of conformational changes. Our HS-AFM imaging results show that these conformational changes occur stochastically.
Requested task
| The proteins are imaged in liquid solution and therefore needs some processing like alignment, noise reduction before any dynamical analysis. Afterwards, these videos need to be analyzed with an autonomous or semiautonomous approach to reduce analyzer dependent bias. There is no available software to do dynamic analysis of conformational changes in HS-AFM videos. With the help of Centuri Engineering platform, we will develop ImageJ plugins to perform automatic data processing and dynamic analysis of the HS-AFM videos. |
Applicant: Mathieu Fallet
Institute: CIML
Engineer: Thomas Boudier
Submission date: 13/10/2021
Summary
We have developed a software, called SAPHIR (F1000Res.2020 Oct 27), with Shiny and R, that allows to easily display and interact with scatter plots of measurements of analyzed objects in 2D images. This allows us to easily define sub populations of objects, not unlikely gating in flow cytometry analysis. We would like to extend this software to have the possibility to work on 2D or 3D images, and manage a large number of images and objects. We propose to implement a Database architecture to store more robustly all information, images, objects, and measurements.
Requested task
| The project need SQL database implementation to interface between labelled images produced by segmentation (ex cellpose) in order to produces measurements used in SAPHIR to define cells populations. A second part could be to develop be a more robust implementation of SAPHIR (in java, python ?) to process multiple images using gating strategy. |
Applicant: Mar Eroles
Institute: LAI
Engineer: Thomas Boudier
Submission date: 20/06/2022
Project summary
Monocytes are suspended white blood cells that flow with the blood torrent. Monocytes become adherent cells after activation, migrate to the site of injury or inflammation and differentiate into macrophages. The mechanical and morphological changes during differentiation into macrophages are still not well understood. Here, we measured the viscoelastic properties and the adhesion of the cells and quantified its morphology using atomic force and interference contrasts microscopy. In addition, we used holographic imaging, a label-free microscopy technique that can differentiate membranes in biological samples in 3D. We used it to characterize better the changes in cell morphology over time.
Requested task
Holographic imaging acquisition datasets are composed of 3D+time image stacks. We want to ask for help from Centuri to use the stacks to reconstruct the volumes of the imaged cells. After the cell membrane is reconstituted in 3D, we would like to extract other parameters such as volume, surface, roughness, membrane protrusions, and the number of internal vesicles.
Applicant: Floriane Cannet
Institute: IBDM/CPPM
Engineer: Thomas Boudier
Submission date: 20/10/2022
Project summary
Our aim is to study the efficacy of combinatorial treatments targeting both immune checkpoints and cancer cells using the Alb-R26Met genetic mouse model of liver cancer, generated in our lab.
Tumor evolution was followed by micro photon-counting computed-tomography (micro PC-CT) for longitudinal in vivo imaging and precise qualitative/quantitative volume analysis. Thus, tumors were segregated into two distinct groups: evolving or regressing/quiescent. At end point, dissociated cells from tumors were processed for spectral single-cell cytometry to assess the immune and tumoral components. Outcomes of these analyses will help us to understand the differences between evolving versus regressing tumors and potentially predict responsiveness/resistance to a treatment.
Requested task
We aim to correlate/integrate the information obtained from imaging analysis and spectral single-cell cytometry by bioinformatics. In order to find if there is a correlation between immunity component and evolution of the tumors (evolving/regressing), to understand why some tumors are responders or not to the treatments, even if located in the same mouse liver. For most tumors, we have corresponding images of dissected tumor and hence outcomes of spectral cytometry. Regarding the imaging, we analyzed so far the volume of the tumors, but we suspect that the localization of the tumor can also play a fundamental role in the prediction.
Applicant: Matthieu Cavey
Institute: IBDM
Engineer: Mathias Lechelon & Benoit Dehapiot
Submission date: 23/10/2020
Summary
My project aims at understanding the genetic, molecular and cellular modifications of the nervous system which drive the evolution of novel behaviors over evolutionary timescales. I use two fruit fly species - D. melanogaster and D. suzukii – that respond differently to chemosensory cues when choosing a substrate suitable for laying their eggs. Using genetic tools, my goal is to compare homologous neuronal circuits functionally across these species and identify the neuronal/circuit differences underlying behavioral divergence in the peripheral and/or central nervous system. This involves behavioral assays, neuro-anatomical analyses, the use of neuronal activity sensors (calcium imaging) and genetic screens.
Requested task
| This project entails developing an imaging system and an image analysis pipeline for quantitative analyses of egg-laying behavior. The imaging setup will be made of multiple cameras controlled by Raspberry Pies. The fruit flies are housed in transparent plexiglass behavioral chambers with agar-based egg-laying substrates at the bottom and illuminated from beneath. A custom mounting system will be developed for the cameras to be used in two applications: (i) automatic counting of eggs at the end of experiments and (ii) automatic tracking of flies during experiments. The system will be adjustable to behavioral chambers of different dimensions. |
Applicant: Marine Tessier
Institute: INMED
Engineer: Benoit Dehapiot
Submission date: 14/10/2022
Project summary
Microglial cells are the resident immune cells of the CNS. One striking feature of these cells is their highly dynamic nature under both normal and pathological brain conditions. Our goal is to measure their dynamic in control condition and after a traumatic brain injury.
Requested task
We have 4D image stacks acquired by bi-photonic microscopy from control and TBI animals, and we need an analyse of the elongation / retraction of microglial processes.
Applicant: Marie Poulain-Zarcos
Institute: CINaM
Engineer: Benoit Dehapiot
Submission date: 31/08/2022
Project summary
The reduced deformability of red blood cells (RBCs) in patients with sickle cell disease induces increased blood viscosity and leads to painful vaso-occlusive crises. The deformability of RBCs influences their spatial organization under flow and the resulting rheology of the blood. To better understand the micro-macro link, an experimental approach is proposed using a microfluidic device and optical techniques to characterize the microstructure of confined RBCs under flow for healthy and rigidified RBCs. To ensure statistical convergence of the measurement for hematocrit values up to 20% (several thousand images), reliable image segmentation is required.
Requested task
The objective of the project is to optimize the post-processing and segmentation of the images in order to automatically process the large amount of images needed to ensure statistical convergence of the microstructure of Red Blood Cells (RBCs). To characterize the microstructure of RBCs, the centroid of each cell is required, as well as their size and orientation with respect to the flow..
Applicant: Karine Magalon
Institute: IBDM
Engineer: Thomas Boudier
Submission date: 07/07/2022
Project summary
Multiple sclerosis (MS) is an inflammatory demyelinating disease of central nervous system leading to irreversible neuronal damage and consequently clinical disability. A histopathological hallmark of MS lesions is myelin damage due to the destruction of oligodendrocytes. We would like to analyze myelin ultrastructure from mouse model of MS using cuprizone intoxication.
For this purpose, we have obtained electron micrographs of cryofixed brain slices using high-pressure freezing and we aim to characterize structural details of the axon/myelin unit in the corpus callosum, prefrontal cortex and fimbria of healthy and cuprizone-treated mice at different time-points.
Requested task
From a dataset of electron micrographs, we need to determine the myelin sheath thickness by creating a pipeline to semi-automatically quantify 1/ the number of myelinated axons out of the total number of axons and 2/ the myelin G-ratio (Axon diameter/Myelinated Fiber diameter).
Also, we would like to use electron tomography to resolve the 3D structure of axon/myelin unit and illustrate/visualize myelin alterations. For this, we need to design a script.
Applicant: Mathieu Fallet
Institute: CIML
Engineer: Thomas Boudier
Submission date: 31/01/2023
Project summary
Realiser un programme (plugin ImageJ) pour recouper des masques de segmentation provenant de différents canaux et intégrer le plugin dans un script groovy pour Qupath dans le cadre d'une analyse d'images/phenotyping de lympho node (Laurine Binet/Pierre Millepied)
Requested task
Plugin java
Script groovy pour quapth
Applicant: Nicolas Buzhinsky
Institute: LAI
Engineer: Thomas Boudier & Thang LE
Submission date: 24/05/2023
Project summary
High-speed Atomic Force Micrsocopy (HS-AFM) is a technique able to visualize biological specimens with nanometer spatial and sub-second temporal resolutions, providing real-time observation of the structural dynamics of biological molecules and assemblies. Typically, an AFM measurement outcome consists of a substantial amount of image sequences data (movies) to be stored, managed, processed and analyzed, preferentially with an autonomous or semiautonomous approach to reduce analyzer dependent bias. At present, there is still no available software providing such an integral treatment of HS-AFM videos.
With the help of Thomas Boudier of Centuri Engineering platform, we have been developing ImageJ-based solutions to perform automatic data processing and analysis of AFM data. These projects include:
#IDP25 - Analysis of HS-AFM movies to understand the structural dynamics of CDH23 and PCDH15 protein.
#IDP16 - Analysis of HS-AFM videos to tackle the dynamics of SARS-CoV2 Spike protein
#Analysis of interaction of bacterial PimA molecules with bio-mimicking supported lipid bilayers.
At the same time, there is a call from our team members for deepening their knowledge of the ImageJ software with the stress on processing and analysis of AFM data, which would make the application of the above-mentioned tools more efficient. Thus, a good generic introduction into basic functionality of ImageJ to lay down a solid basis and eventual continuation into the processing, analysis and automation for AFM movies would be highly beneficial.
Requested task
An introductory two-day course on image processing and analysis with ImageJ, with the following tentative program:
Day 1:
- Overview of ImageJ interface, basic operations
- Analysis of image histograms
- Filtering for noise reduction
- Compensation of imaging artifacts specific to AFM:
- line by line flattening
- drift correction
- noise reduction
- parachuting compensation
Day 2:
- Object measurement and quantification
- Automation of processing and analysis of AFM image sequences (movies)
- Data storage and management
Applicant: Pascale Chavis
Institute: INMED
Engineer: Thomas Boudier
Submission date: 25/02/2022
Project summary
The brain extracellular matrix serves multiple functions in the brain throughout life and has also emerged as a psychiatric risk factor in a wide spectrum of psychiatric disorders. Two key players in this context appear to be the glycoprotein reelin and perineuronal nets. They critically contribute to postnatal central nervous system maturation, plasticity and functions and have been implicated in the etiology and pathophysiology of major psychiatric disorders, e.g., schizophrenia, major depression, bipolar disorders. Our goal is to address the anatomical organization of neurons expressing these extracellular matrix structures during postnatal maturation of the cortex.
Requested task
We would like to develop a 3D analysis pipeline to:
1/ detect cells based on their nuclear marker, automatically count and quantify cells identified by one of two the markers from a dataset of confocal fluorescent images. The general protocol will include definition of specific threshold for the different signals, images segmentation and analysis of shape, geometry and pixel intensity of objects.
2/ map the 3D anatomical organization of cells identified by one of two the markers by characterizing the relationship e.g., distance and interactions, between objects within a population.
3/ detect and analyse spots within the different detected objects.
Applicant: Prithwidip Saha
Institute: LAI
Engineer: Thomas Boudier
Submission date: 29/03/2023
Project summary
Hearing in vertebrates relies on the inner ear mechanotransduction process. Cadherin-23 (CDH23) and protocadherin-15 (PCDH15), non-classical members of the cadherin protein family, are directly involved in this process. High-resolution structural models of both proteins have been established using x-ray crystallography and molecular dynamics simulations. However, real-time observation of the structural dynamics of these individual proteins is yet to be accomplished. In this work, we use high-speed atomic force microscopy (HS-AFM) imaging to visualize the structural dynamics of full-length ectodomains of CDH23 and PCDH15 on mica at nanometer spatial and sub-second temporal resolutions.
Requested task
We would like to analyze the different protein structures and their dynamics obtained in the HS-AFM movies by extracting important parameters such as contour length, end-to-end distance, minimum and maximum curvature, etc. Due to the unavailability of a robust plugin to perform such a task, we aim to develop ImageJ-based macro(s) which also take into account image pre-processing like background subtraction, tilt correction, and noise reduction. Utilizing the CENTURI multi-engineering platform, our goal will be to build ImageJ-based plugins capable of conducting semi-automated data processing and analysis of the HS-AFM movies.
Applicant: Sophie Chauvet
Institute: IBDM
Engineer: Thang LE
Submission date: 19/04/2023
Project summary
The team " Neural plasticity in cancer development" at IBDM, studies how neuronal plasticity and function regulate cancer progression in mouse models of pancreatic ductal adenocarcinoma (PDAC). We discovered that axons from different components of the peripheral nervous system innervate precancerous lesions and invasive cancers. We are also exploring how peripheral nerves may lead to accelerated or reduced tumor progression depending on their neurochemical properties.
Requested task
Given the multi-faceted role of the different components of the peripheral nervous system in modulating PDAC progression, neuronal fibers represent an attractive target to curb tumor development and progression. We are using 3D light sheet fluorescence microscopy to visualize in whole pancreas the architecture of neural networks, their interactions with the tumoral microenvironment and tumor progression. However, manual reconstruction of the pancreatic tissue is a tedious and time-consuming task. The main goal is to provide a tool to help segmenting and visualizing in 3D the whole pancreas.
Applicant: Françoise Muscatelli
Institute: INMED
Engineer: Thang LE
Submission date: 24/05/2023
Project summary
Cell counting is a time consuming process if done manually. If it is done with image processing software (Image J, Fiji ..) it can be automated but we have observed a considerable number of errors due to the change of shapes when the density of the objects (cells) to be counted increases. After an automated count, we check the error rate, which is also very time consuming. We would like to have an automated counting system that is reliable and reproducible.
Requested task
Based on the images provided for counting cells, evaluate the different applications/programs available to see which one would be most suitable for determining a cell count from another population of reference cells (using coloured markers). Consider whether the counting (by decreasing the error rate) could be improved by a deep learning approach to recognise errors.
MECHATRONICS
Applicant: Sofia Zangila
Institute: INMED
Engineer: Fabrice Dessolis
Submission date: 04/07/2024
Summary
The goal of this project is to create a custom-made headplate for a developmental neuroscience lab.
In our lab we study neuronal activity across development with 2-photon in-vivo microscopy and try to assess its role in the
functional maturation of the underlying neural circuits.
To do that we perform cranial window implantation surgeries on mouse pups. The surgery involves surgically attaching a
headplate on the cortex and removing a part of the cranium to allow for optical (laser) access during 2-photon microscopy. Up to
now we have been using an aluminium headplate of 4mm inside-diameter and approximate weight: 0.3 gr (manufacturer: Luigs
and Newmann).
In this project we are interested to construct a more suitable headplate for cranial window implantation surgery for mouse pups.
As such, we will use a light(er) material to fabricate a new heaplate and facilitate post-surgery development for the mouse pups.
Applicant: Jérôme Belougne
Institute: CIML
Engineer: Mathias Lechelon & Guillaume Gay
Submission date: 15/07/2020
Summary
Optimize the automation of the image capture already present ( DMS300 / Workstation Tecan gemini).
The aim of the optimization will be to replace the currently used automaton with an X-Y automated platform system.
Create a plexiglass enclosure to control the environment (humidity, temperature) around the camera and the X-Y platform.
Optimize the imaging instrument, to obtain higher quality images.
Applicant: Anne Charrier
Institute: CINaM
Engineer: Mathias Lechelon
Submission date: 07/12/2020
Summary
We propose a technological breakthrough to manufacture submicron wide slits (from 0.1 micron) with high aspect ratio in microdevices. These microdevices enable the observation by optical video-microscopy of the behaviour, migration or passage/blockage of cells and micro-organisms in these slits, under the effect or not of a microfluidic flow. This technology is to be valorised by a start-up, ICOVELL, to be created in the last quarter of 2021. Today, quantitative studies are limited by the artisanal approach to the manufacture of the slits. We need to improve slits dimension reproducibility and to develop parallelized processes for increased production (small scale).
Requested task
The key technological point is to control the chemical etching with high precision. To reach this goal we need to develop a prototype instrument of a chemical etching system allowing very precise control of temperature (0.1°C at least), concentration and intimate mixing of non soluble solutions. The system will be built of different parts. 3D printing will be used to make the wafer holder and stirring system. A mecatronics enginer is required for the project.
Applicant: Nagham Badreddine
Institute: INMED
Engineer: Mathias Lechelon
Submission date: 04/07/2022
Summary
Social interactions underlie various behaviors such as cooperation, group coordination, mating and protection. Most of these behaviors rely on forming social memories, i.e., to remember familiar conspecifics, a process that can be affected in autistic syndromes. Mice have been shown to form such memories and optogenetic studies have demonstrated that assemblies of excitatory neurons in a region of the hippocampus (ventral CA1) constitute a primary site of social memory. However, how selected types of social interactions are precisely represented at the level of the networks and whether these neural representations are altered in autism remain largely unknown. The project aims to use a last generation miniature microscope to record neural activity (via calcium imaging) of large neural ensembles of different cell types in ventral CA1 of awake mice during a validated social investigation paradigm.
Requested task
1) In order to image calcium activity in the ventral CA1, we need to implant a lens at a steady speed without saccadic movements. We would like to eliminate the variation caused by manual implantation. Task: To use a precision stepper motor for stereotaxic lens implantation.
2) In our project we use a miniature microscope to record neural activity in freely-moving animals. The problem is that the cable twists when the animal rotates which then affects the movement of the animal. Task: To create a commutator based on a home-made model.
3) Laser-cutting a slit in a transparent tube to test dominance between animals while imaging.
Applicant: Ede Rancz
Institute: INMED
Engineer: Mathias Lechelon
Submission date: 14/10/2022
Summary
This project is to build a rotation platform for experiments in mice, documented here: https://ranczlab.github.io/RPM/.
Requested task
3D printing and laser cutting the required parts.
Applicant: Philippe Roudot
Institute: I2M
Engineer: Mathias Lechelon
Submission date: 25/11/2022
Summary
Our study will be focusing on the factors triggering locomotion in trichoplax adherens (TA) in collaboration with Andrea Pasini. Our preliminary work during the 2022 Centuri hackathon has focused on testing new approaches for TA's imaging and tracking across multiple scales using a custom and low-cost microscope. In combination with real-time stochastic inference approaches for multiple object tracking, we showed that step-wise stage motions are precise enough to follow TA displacements, but that the device is currently too limited for the joint imaging of cellular object and animal shape changes. Together with Matthias, we will be designing a prototype for low-cost multi-scale microscope adapted to the size and dynamics of the biological process and the capacities of our computational tracking approach.
Requested task
1. Implementing and testing the existing fluorescence module.
2. Collaborative design of a dual-objective device.
3. Implementation of a dual-objective device.
4. Incremental design improvement toward ventral cells imaging.
Applicant: Juliette Contadini
Institute: INMED
Engineer: Fabrice Dessolis
Submission date: 26/07/2023
Summary
For my brain slices electrophysiology experiments, the brain must be cut according two angles : a coronal angle of 30° and a dorso-ventral angle of 10°. This is currently done manually, using a razor blade and cutting block made of agar, used as a slope guide of 10°.
The agar cutting guide is flexible which can induce a bias while cutting and is also damaged by the repetitive cut throughout experiments as the razor blade sometimes alters its surface.
Requested task
The agar guide block is not an optimal tool. It is not long-lasting and its flexibility does not allow the cration of a precise 10° angle.
The creation of a cutting block either 3D printed or build in another more resistant material could really help to perform the experiments described before and the reproduciability of these lasts.
Applicant: Qiyan Mao
Institute: IBDM
Engineer: Fabrice Dessolis
Submission date: 18/10/2023
Summary
Mechanical forces play crucial roles during development and homeostasis of muscles. Our previous study has revealed that human myofibers spontaneously form bundles in vitro, which transit from a dynamic to a stably attached state (Mao, Acharya et al. eLife, 2022). At this transition, tensile forces are high and contractile sarcomeres emerge within myofibers. We hypothesise that mechano-transduction pathways can detect tension levels to trigger intracellular sarcomere assembly, and hence the state transition in muscle bundles after successful attachment. Here, we aim to characterise how sarcomere assembly and mechanotransduction pathways respond to defined external mechanical stimulations of the myofibers, in order to uncover the molecular underpinnings of tension-sensing mechanisms.
Requested task
To manipulate tension levels on muscle bundles, we will build a cell stretcher, and apply static or cyclic uniaxial stretches on differentiating muscle bundles. We will follow the dynamic incorporation of key sarcomeric components. In parallel, we will collect control and stretched muscle bundles samples, to perform transcriptomic analysis. Together, this will allow us to take a systematic approach to uncover genome-wide molecular changes in muscle bundles following tension manipulation, to identify activated mechano-transduction pathways controlling sarcomere assembly.
Finished projects
Applicant:Sébastien Mailfert
Institute: CIML
Engineer: Mathias Lechelon
Submission date: 10/09/2020
Summary
Reaching a nanometer precision in molecular localization using Single Molecule Localization Microscopy is not possible without taking care of each step (sample preparation, data acquisition and analysis).
The drift correction of sample is critical and is classically performed offline, after the acquisition of the data. If one can be able to do it in real-time, this will save lots of time and ambiguity if correctly done.
Requested task
In this context, we are building a dedicated system which requires a XYZ piezo system. Unfortunately, the manufacturer does not provide a sample holder.
The task is to design a sample holder which requires to be stable, easy to use, not too heavy allowing a simple and robust sample fixation.
We can begin with a 3D printing design if it is sufficient.
Applicant: Long-Fei Wu
Institute: LCB
Engineer: Sophie Brustlein & Mathias Lechelon
Submission date: 15/07/2020
Summary
Illumination with UV and violet light can change swimming velocity of multicellular bacteria in magnetic field. We need implement a custom-made microscope to determine the wavelength (energy) and irradiance (number of photons) require for triggering the photokinesis behavior.
Requested task
Need the help of optics and biophotonics engineer to modify the current design and construct the microscope, and mechatronics engineer to 3D print condenser and sample holders.
Applicant: Mathieu Fallet
Institute: CIML
Engineer: Mathias Lechelon
Submission date: 08/07/2020
Summary
Intravital organ microscopy allows visualization of B cells in the lung after viral infection (Mauro Gaya team). This phenomenon is complex both in terms of locating the area to be imaged and controlling the focus, and requires recordings lasting more than an hour. As a result, the image must be stabilized throughout the recording in order to be able to visualize the movements of the cells over fairly long periods of time. Commercial microscopes (here a Leica SP5) are not open about the possibility of external focus control; autofocus is sometimes available but is not effective for this project. We would like to compensate for the Z-drift due to the crushing of the sample over time by controlling the microscope's remote control knob with a motor. The speed should be calculated beforehand and easily changed during the experiment, and a stop should be set to prevent the objective from being crushed on the sample. An easily accessible STOP button would also be very useful in case of problems.
Requested task
The idea is to build a motor that will fit the Z-axis knurl of the two-photon microscope in order to change the focus constantly to correct the drift, due to the crushing of the sample (that will have to be calculated beforehand). This will not prevent the use of the joystick. A stop should be set so the objective does not damage the specimen, depending on the working distance of the objective used (here a 25x Leica), and an easy to use STOP button could be placed next to the computer.
Applicant: Jorge Rodriguez Ramos
Institute: LAI
Engineer: Mathias Lechelon
Submission date: 23/10/2019
Summary
We are developing new equipment in our laboratory. One part of the development includes home-building our atomic force microscopy (AFM) head, to study biological samples (cells and tissues). Another requires a petri dish heater to keep the samples at 37 degrees during the experiments
Requested task
We need help with a group of tasks related to 3D modelling. The AFM head's development and the petri dish heater requires the 3D printing and computer numerical control machining of prototypes to test different future system configurations.
Applicant: Rémi Lasserre
Institute: CIML
Engineer: Mathias Lechelon
Submission date: 05/08/2020
Summary
In vivo, T cell activation is initiated by sequential and short-lived interactions with Antigen Presenting Cells (APCs). Different dynamics of T cell/APCs interactions (duration, frequency) have been associated to different activation outcomes (Immunity vs. tolerance). However, due to technical limitations, the causal link between signal dynamics and activation outcome is not formally demonstrated yet.
We recently developed an efficient recombinant optogenetic system to reversibly trigger T cell Receptor signaling with light. Our goal is now to generate a versatile illumination toolbox to provide specific stimulation patterns to T cells and analyse how they influence their activation outcome.
Requested task
We would like that the Centuri mechatronician help us for the design and the realization of an illumination tool box able to generate specific temporal pattern of illumination to T cells in cell culture plates (24 well plates for exemple). This box should have the capacity to provide an independent control for each well of :
- The light power
- The temporal pattern of illumination
- The light wavelength by using 2 type of LEDs (660nm for light induced TCR aggregation, and 730 nm for the reversion of this process).
Applicant: Laurent Fasano & Françoise Muscatelli
Institute: IBDM & INMED
Engineer: Mathias Lechelon
Submission date: 17/04/2021
Summary
Machine learning and computer vision (CV) tools allow automatic detection and quantification of mice behaviors, including mouse models of autism spectrum disorder (ASD). The project aims at building a Live Mouse Tracker system (LMT-https://livemousetracker.org) to develop new, objective behavioral metrics, which is key for understanding neural systems and behavior relationship
Requested task
Advise and supervise an M2 student from Central Marseille in the assembly and tuning of the LMT.
Applicant: Alla Sollod & Epsztein/Rouault
Institute: IBDM & INMED
Engineer: Mathias Lechelon
Submission date: 07/06/2021
Summary
Animals can flexibly navigate their environment by computing different paths to similar targets. To date, spatial navigation has been well-studied in rodents navigating small, un-cued laboratory environments. However, the mechanisms of large-scale navigation in more complex, cue-rich environments are far less understood. Place cells in the hippocampus, a key structure for spatial navigation, are pyramidal neurons that fire action potentials whenever an animal is at a specific position within its environment. During large-scale navigation, different parts of the environment could be coded at different spatial resolutions. This hypothesis is difficult to test in regular-sized laboratory environments. We propose to take advantage of newly developed virtual reality systems for rodents to study large-scale spatial navigation. The project will combine behavioral analyses using virtual reality for rodents, multisite recordings of neuronal activity in the dorsal hippocampus, and computer modeling
Requested task
To study large-scale spatial navigation we developed a virtual reality set-up. We used Unity software to design a virtual environment, inside which animals could navigate while running on the SpeedBelt. The neuronal activity from the hippocampus is recorded using a 64-channels Buzsaki probe and acquired at the OpenEphys acquisition board. For further analysis, the high precision of recorded neuronal signal aligned with a position in VR is crucial. For this, we would like to send position data (previously acquired with a SpeedBelt) from the Unity virtual environment to the OpenEphys acquisition board. Position data sent to the Arduino board should range from 0 to 65535 (in mm).
For this, the Arduino Uno board with a DAC module would be connected to the Unity software and send the encoded position as an analog signal to the OpenEphts acquisition board.
Also, 3D printed boxes for projects in Arduino Uno and Arduino Mega 7 (for reward delivery in VR) are needed
Applicant: Nihaad Paraouty & David Robbe
Institute: INMED
Engineer: Mathias Lechelon
Submission date: 25/06/2021
Summary
Navigation through space is a fundamentally complex behavior displayed by many animals. It relies on both fast learning and the integration of multiple cues to decide among many possible actions. Animals and humans often have to take navigational decisions based on salient sensory information with various degrees of certainty, depending on their familiarity with the surroundings and their past decision outcomes. For instance, in a familiar setting, a hungry mouse will naturally use its whiskers in the dark to gather key sensory cues and take navigational decisions such as turning left/right or running straight in order to quickly reach a known food source. In contrast, when placed in a novel, unfamiliar environment, the mouse being less certain of its navigational foraging decisions, will slow down, take seemingly random turns and hesitate at different intersections. In this project, we posit that striatal medium spiny neurons of the direct and indirect pathways mediate such sensorimotor certainty of navigational decisions through competing co-activation. Using a combination of animal behavior (navigation and foraging task) and closed-loop optogenetic stimulations, we propose to study this question.
Requested task
1. Development and setup of a mouse maze (use of laser cutting machine and 3D printer)
2. Development and setup of water rewards in the maze (use of 3D printer)
3. Video acquisition and closed-loop stimulations setup (customizing 2 open-source softwares: Autopilot and DeepLabCut-live)
Applicant: Long-Fei Wu
Institute: LCB
Engineer: Sophie Brustlein & Mathias Lechelon
Submission date: 06/10/2020
Summary
We have isolated marine bacteria of which the growth is boosted by infrared. We wish to monitor the growth and absorption of the cultures on real time.
Requested task
Design and construct, together with Sophie Brustlein, a illumination system that allow measuring growth and light absorption on real time.
Applicant: Victor Tsvirkun
Institute: Fresnel
Engineer: Mathias Lechelon
Submission date: 12/08/2020
Summary
Creating a demonstrator prototype for using multimodal flexible imaging (FIP) probe, we have to design, assemble and interconnect different modules (optics, electronics, etc.) within the rackmount system. Such a design would allow for a compact system while keeping the modularity and being able to integrate into different existing experimental set-ups or to operate in a completely standalone mode.
Requested task
We outlined several tasks after a briefing with our associated CENTURI engineer, including both the design of the internal layout of the abovementioned rackmount modules and fabrication of the parts (employing 3D printing and CNC milling) required for the final assembly of all the components inside the modules. An additional effort would be allocated to prototyping the working surface situated at the top of the rackmount system, first adapting an existing breadboard and next designing and milling a dedicated fully-customized piece in-house.
Applicant: Matthieu Cavey
Institute: IBDM
Engineer: Mathias Lechelon & Benoit Dehapiot
Submission date: 23/10/2020
Summary
My project aims at understanding the genetic, molecular and cellular modifications of the nervous system which drive the evolution of novel behaviors over evolutionary timescales. I use two fruit fly species - D. melanogaster and D. suzukii – that respond differently to chemosensory cues when choosing a substrate suitable for laying their eggs. Using genetic tools, my goal is to compare homologous neuronal circuits functionally across these species and identify the neuronal/circuit differences underlying behavioral divergence in the peripheral and/or central nervous system. This involves behavioral assays, neuro-anatomical analyses, the use of neuronal activity sensors (calcium imaging) and genetic screens.
Requested task
| This project entails developing an imaging system and an image analysis pipeline for quantitative analyses of egg-laying behavior. The imaging setup will be made of multiple cameras controlled by Raspberry Pies. The fruit flies are housed in transparent plexiglass behavioral chambers with agar-based egg-laying substrates at the bottom and illuminated from beneath. A custom mounting system will be developed for the cameras to be used in two applications: (i) automatic counting of eggs at the end of experiments and (ii) automatic tracking of flies during experiments. The system will be adjustable to behavioral chambers of different dimensions. |
Applicant: Didier Tonneau
Institute: CINaM
Engineer: Mathias Lechelon
Submission date: 08/03/2021
Summary
This project aims to demonstrate the feasibility of a hard X-ray fibered camera (from 2 keV to 20 MeV). Each pixel is made of an optical fiber equipped with a scintillator element. The fibers must be assembled into an n x n matrix using a plastic fiber holder to avoid any metal interaction with the X-ray beam. Furthermore, the required machining dimensions are not compatible with conventional means of fabrication.
Requested task
Design and Manufacturing by 3D printing of a fiber optic carrier resulting in a row of 16 aligned fibers.
This strip must be removable to be able to change the fibers in case one of them is broken. The bar must be able to be mounted in a vertical or horizontal position on an X, Y, Z displacement table. Indeed, the CINaM team is working with several beam geometries on different sites.
Applicant: Alla Solod
Institute: INMED
Engineer: Mathias Lechelon
Submission date: 13/10/2021
Summary
Animals can flexibly navigate their environment by following different paths to similar goals. This ability is thought to rely on an internal cognitive map. Place cells in the hippocampus, a key brain structure for spatial navigation, are pyramidal neurons that fire action potentials whenever an animal is at a specific position within its environment (their place field). Place cell coding and navigation have been studied for decades in small (e.g. 1m in size) homogeneous (in terms of local cues) environments. However, in the wild animals including rodents can navigate several kilometers away from their home base to food location through inhomogeneous landscape. During such large-scale navigation, different parts of the environment could be coded at different spatial resolutions through "nested hierarchies" of coarse and fine grain coding with large and small place fields observed for the same neurons (Eliav et al., 2021). However, it is unclear how place fields size and number are influenced by specific features of the environment such as the availability of local/distal sensory cues and rewards.
To address this question, we developed a behavioral task where head-fixed mice perform 1D spatial navigation in a semi-realistic 2D virtual environment with inhomogeneous distribution of visual cues and rewards. This setup will allow us to systematically and reliably vary the factors that influence spatial coding (e.g. distal/proximal visual cues, rewards) while recording the activity of hundreds of place cells using silicon probes.
Requested task
We would like to have a new reward-delivery system that would allow us to suck back the drop of reward (sugar water) if the animal did not take it in a reward zone. Also, we would like to have the same size of drops during the session and being able to easily modify it if needed.
Applicant: Valentin Dunsing
Institute: IBDM
Engineer: Mathias Lechelon
Submission date: 19/10/2021
Summary
The aim of the project is to build a sample chamber for a single-objective light sheet microscope (soSPIM). In this technique, the sample is illuminated by a horizontal light sheet, which is created by reflection on micro-fabricated gold mirrors that are part of the culture dish. To achieve multi-view imaging, the sample is illuminated from multiple sides, requiring accurate alignment and therefore planarity of the culture dish. In this project, a new 3d printed magnetic chamber will be designed, replacing the current design that is prone to tilt of the sample, causing misalignment artifacts.
Requested task
- Design prototype chamber
- 3d print components
- Assemble chamber
- Best and improve prototype
- Construct multiple chambers
Applicant: Valery Matarazzo
Institute: INMED
Engineer: Mathias Lechelon
Submission date: 24/01/2023
Summary
The project is to model maternal exposure to pyrethroids in pregnant mice and assess in the progeny ASD-like phenotype.
We need to design an exposition chamber in which mice will inhale insecticides.
Requested task
We need to design an exposition chamber in which mice will inhale insecticides. This chamber should have a size of 50*30*20 (24l) and is made of plexiglass and will contain holes for air entry and air exit. From the top, an openable cover with waterproof closure should exist in order to access inside the chamber.
The chamber should contain a pre-chamber for insecticide dilution of size 10*30*20.
A building plan will be sent by email.
We also need to make a feeder and a bottle holder by 3-D printing.
Applicant: Arthur Coët
Institute: MIO
Engineer: Mathias Lechelon
Submission date: 06/04/2023
Summary
Diazotrophs have the ability to fix nitrogen gas into ammonium and are sustaining ~50% of the primary production in the ocean. Diazotrophs can be photosynthetic cyanobacteria or non-photosynthetic bacteria (the latter called non-cyanobacterial diazotrophs or NCDs). Marker gene and genomics approaches suggest that NCDs dominate in the oceans. Devoid of a photosynthetic apparatus, NCDs are forced to obtain organic matter and energy from external sources, of which particulate organic matter are the main suspect. Nitrogen fixation in high-latitude cold waters is thought to be mainly driven by NCDs, as the environmental conditions inhibit cyanobacteria. During the summer of 2023, an oceanographic campaign will take place in the Arctic Ocean where we aim at studying the dynamics of particle colonization by NCDs. To this end we will deploy an ISCA device (Lambert et al., 2017). This device is a small plate (90 mm x 100 mm x 8 mm) composed of 25 wells, each with a lid, thus allowing to put substrate or synthetic particles inside, which allows the in situ incubation of seawater and the eventual colonization of these artificial particles by various microorganisms over time.
Requested task
The aim of this project is to use CENTURI's Markerspace to 3D print and laser cut a device for the observation and analysis of NCD chemotaxis towards organic matter particles in situ.
- Design of the ISCA in PMMA
- Laser cutting of PMMA plate to build an aquarium for the incubation of the ISCA
The design of the ISCA will be redesigned and made of PMMA, allowing several uses during the cruise, as well as the possibility to sample at different times. The aquarium will be designed to be suitable and resistant for use on a boat. Using laser cutting, including a double wall allowing to slide in filters to mimic the light present to which the NCDs will have been sampled. Research into the optimum materials to be used (screws, joints, etc.) will also be taken into account for this project.
Applicant: Didier Marguet
Institute: CIML
Engineer: Mathias Lechelon
Submission date: 06/11/2023
Summary
Development of a part for adjusting the focus in samples of molecules in solution for long FCS recordings as part of the European LINkS project.
Requested task
Develop a mechanical part to modify the focus as discussed during Mathias' visit.
MICROFLUIDICS
Finished projects
Applicant: Etienne Loiseau
Institute: CINaM
Engineer: Pierre Bohec
Submission date: 02/03/2022
Summary
We study mechanical properties of red blood cells by using a microfluidic chip.
The goal is to design and engineer a double connector to injects two different fluids at the single inlet of a microfluidic chip.
A solution has been found with commercial connector injecting the two fluids from the same inlet.
Applicant: Olivier Theodoly
Institute: LAI
Engineer: Pierre Bohec
Submission date: 03/03/2022
Summary
Microfluidic devices to control gradient without flow.
Requested task
- UV lithography in clean room using combination of different resins (AZT, SU8)
- Optimize soft lithography process for multi-layer PDMS chip
Applicant: Sham Tlili
Institute: CIML
Engineer: Pierre Bohec
Submission date: 28/04/2022
Summary
Mechanical constraints have a high impact on development processes, and there is a need for new tools to investigate the role of mechanosensitive pathways in tissue reorganization during development. We want to develop here experiments where embryonic cell aggregates are aspired through constrictions in microfluidic channels, generating heterogeneous flows and cell deformations that can be imaged using biphoton microscopy. This tool provides a way to measure in situ local viscoelastic properties of 3D tissues and connect them to intercellular and extracellular events such as cell shape changes and cell rear-rangements. Perspectives include applications on organoids to investigate and quantify rheological properties of tissues, and to understand how constraints affect development.
Requested task
The microfluidic device has been already developed with a thickness of 80 to 100 microns. However, given the size of aspired aggregates, we would need higher aspect ratio microfluidic channels.
Indeed the hight would need to vary more in a range of 100 microns to 200 microns with contrictions in the xy plan around 20-50 microns.
For that, classical SU8 design could be tried by adding multiple layers. Microdrilling could be also potentially tried.
Applicant: Antoine Barriere
Institute: IBDM
Engineer: Pierre Bohec
Submission date: 17/05/2022
Summary
microfluidics for buffer changes on fixed samples
Requested task
We planned on a PDMS cover to be installed on slides/glass bottom dishes with inserts for buffer changes.
Final solution
A commercial device has been found to be the best solution for this project
Applicant: Marie-Pierre Valignat
Institute: LAI
Engineer: Pierre Bohec
Submission date: 20/05/2022
Summary
Mimicking transwell assay with microfluidics to study the response of T cells to chemokines.
Requested task
- Design and fabrication of a setup mimicking the usual transwell tool used in the study of immune cells
- UV lithography with different resins and different thickness
- multilayer soft lithography
- Series of experiment demonstrating the feasibility and the interest of a tilted microscope
- Integration and automation under microscope : set up of a tilted microscope and design of a graphical user interface for the control for the microvalve with Matlab
Applicant: Nicolas Waisbord
Institute: LCB
Engineer: Pierre Bohec
Submission date: 01/02/2023
Summary
EcoMix (AMIDEX chair of excellence project) targets the impact of mixing features of soil on the transport properties of microbes. By mimicking the chaotic flows characteristic of porous media in model microchips, we aim at observing microbial life in these convoluted environments to understand how chemotaxis, magnetotaxis and niche-partionioning depend upon the heterogeneity of porous media microstructure.
Requested task
- Set up the new microfluidic lab of the LCB. Choose equipment and methods suitable for my project and more widely, for a smooth start of microfluidics at the LCB.
- Fit Helmoltz coils to a standard microscope.
- Realize a few photolithography of classical chips, and help me set up the soft-lithography process in our campus.
- Embarking on the journey to establish a microfluidics chip shop : https://lcb.cnrs.fr/technology/microfluidics/
Applicant: Meriem Djendli / Didier Marguet
Institute: CIML
Engineer: Pierre Bohec
Submission date: 04/05/2023
Summary
We would like to use transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT, a variant of point accumulation for imaging in nanoscale topography) for simple and easy-to-implement multiplexed super-resolution imaging that achieves sub-10 nm spatial resolution in vitro on synthetic DNA structures. Therefore, we would like to implement a multiplexing approach (Exchange-PAINT) that allows sequential imaging of multiple targets using a single dye and laser source.
Requested Task
We would like to install a micro-fluidic system on our super resolution microscope to do PAINT exchange, with 3 channels.
We would need an airtight system, which allows a reasonable flow rate so as not to move the cells during the acquisition.
Applicant: Nathalie Pujol
Institute: CIML
Engineer: Pierre Bohec
Submission date: 06/07/2022
Summary
We are interested in measuring the mechanical properties of worms. Conventional AFM measurements require immobilising C. elegans worms with both anaesthetic and glue on an agarose pad. We have found that the glue step influences the mechanical properties and we would like to switch to microfluidics. source.
Requested Task
Several devices have been designed for adult C. elegans worms PMID: 28207921, PMID: 35320572. This specific device should allow AFM measurements. The probe must have access to the upper part of the worm, the worm must be completely immobilised and the device must not emit vibrations.
Solution
No user-friendly solution was identified, so an alternative option without microfluidics was selected due to its significantly easier setup.
Applicant: Claudia Petrillo / Tâm Mignot
Institute: LCB
Engineer: Pierre Bohec
Submission date: 23/05/2023
Summary
Myxococcus xanthus is a gram-negative bacterium widely distributed in soil. It is capable of moving thanks to two different types of machinery: type IV pilus retraction power the Social motility of groups of cells; focal adhesion complexes guide the Adventurous motility of single cells. It has been demonstrated that fungal hyphae could work as "highways" allowing the displacement of other bacteria in the soil. The aim of this project is to understand if M. xanthus is also able to take advantage of the fungal network to move in the soil, and to unravel the molecular basis of this possible interaction.
Requested Task
What is necessary for this project is to build an environment where to observe the interactions between Myxococcus xanthus and the fungus. For this reason, we thought about a PDMS "porous" chamber that could mimic the soil structure, allowing us to potentially reproduce what occurs at the ecological level. The request is to build a suitable mold for this aim, to set up a microfluidic experiment.
Applicant: Matthieu Bergé
Institute: IM2B/LCB
Engineer: Pierre Bohec
Submission date: 17/05/2023
Summary
Cyanobacteria, that just require sunlight to growth, have a significant impact on natural ecosystems and are strong candidates for biotechnological applications. In this context, Anabaena stands out as a strong contender for hydrogen production. However, to fully harness its potential, a deeper understanding of its physiology is essential. Our objective is to gain insights into Anabaena's physiology by adopting a multiscale approach, ranging from the population level to the single-cell level, using fluorescence microscopy. To achieve this, we will employ microfluidic techniques which offer solutions to various challenges associated with its growth and provide the added benefit of high-throughput capabilities.
Requested Task
We would need a microfluidic engineer to realize some microfluidics molds with very specific heights of 4.5 microns to keeps our large (300 microns long) filamentous (3 to 4 microns wide) multicellular organisms in the same focal plane while perfusing media to observe its growth at 100X which will enable us to resolve intracellular protein localization within each individual cell.
Applicant: Pierre-Henri Puech
Institute: LAI
Engineer: Pierre Bohec
Submission date: 19/06/2023
Summary
Printing a syringe holder to modify an existing setup for Magnetic Particle (MP) manipulations and biomembrane force probing.
Requested Task
Use a 3D printer to make the syringe holder
Applicant: Philippe Robert
Institute: LAI
Engineer: Pierre Bohec
Submission date: 19/06/2023
Summary
We use a microprinting system based of UV illumination to develop single-step leukocytes functional tests for hospital or drug development use. While some of our tests start to function properly , a current bottleneck to deployment in for clinical trials is the very time-consuming process of microprinting due to the many steps of solution depositions, illuminations and rinsing. We aim to automatize this process by developing a microfluidic tool to perform without human help the handling of liquids. Combined with dedicated (and already possible) programming of the microprinting device, an almost completely automatized sample production is at reach.
Requested Task
The task consist first in designing and producing a microfluidic device incorporating control valves allowing to control the flow of several fluids, permitting to fill and rinse a microchamber with four to six different solutions without human help. A second task consists in programming an interface to couple the piloting of the microdevice with the piloting of the micropatterning device.
Applicant: Flora HONORE / Tâm Mignot
Institute: LCB
Engineer: Pierre Bohec
Submission date: 04/09/2023
Summary
Preliminary observations have shown that the bacteria studied by our team (Myxococcus xanthus) is capable of sliding between glass and PDMS obstacles. The idea now is to create microfluidic chips that allow these bacteria to slide under a PDMS ceiling. We are now looking to have larger observation zones and to control the height of the ceiling (1 micrometre minimum). The long-term aim is to study the behaviour of groups of cells in chemotaxis experiments, for example. These chips could also be adapted to study a multitude of bacteria (e.g. cyanobacteria) as well as fungi.
Requested Task
Realize a double photolithography of chips: one for pillars to support the ceiling (from 1 um) and another one for the ceiling (50 um). Photolitho masks will be supplied.
Further photolithography of the chip will probably be necessary to adapt the chips to the microorganisms to study.
Applicant: Olivier Theodoly
Institute: LAI
Engineer: Pierre Bohec
Submission date: 15/09/2023
Requested Task
Develop a DIY optical setup capable of aligning and bonding multi-layer microfluidic devices
OPTICS & BIOPHOTONICS
Applicant: Hervé Rigneault
Institute: Institut Fresnel
Engineer: Sophie Brustlein
This Tech Transfer project deals with the development of a flexible probe that can be handheld or inserted into a small animal and that performs multimodal imaging (1P and 2P and 3P fluorescence, fluorescence lifetime imaging, second harmonic generation (SHG), third harmonic generation(THG) and coherent anti-Stokes Raman scattering (CARS). The proposed project aims at developing an engineer grade version of the multimodal flexible imaging (FIP) probe that has been in development at the Fresnel institute over the last 5 years. The current development has reached TRL4. Most of the technical steps have been demonstrated and validated but the full device remains a demonstrator that cannot be exported in application labs and imaging platforms, neither it can be operated easily with a user friendly interface. We have identified several mechanical, optical, electronic and computer programming steps that need to be addressed to bring the FIP technology to the level of a useable device for the CENTURI community.
Keywords: optical fibered probe, 1P 2P 3P fluorescence, Ca2+ imaging, nonlinear label free imaging
Applicant: Simon Labouesse
Institute: IBDM
Engineer: Sophie Brustlein
Summary
The CENTURIM project aims to develop an original instrumentation (RIM: Random illumination Microscopy) on the Luminy site allowing access to super-resolved fluorescence imaging in biological samples (cells and model systems). This method coming from the Fresnel Institute and recently validated by the Integrative Biology Center of Toulouse has advantages over structured illumination and Airy scan techniques to access super-resolved fluorescence imaging in scattering media. In particular, very promising results have been obtained in model systems (drosophila) suggesting the broad use of this new imaging modality by the CENTURI community. The project as presented consists in building a RIM microscope and developing the algorithms and codes necessary for the reconstruction of super-resolved and sectioned images. A three-dimensional extension of RIM is also envisaged in collaboration with the Fresnel Institute.
Requested task
We propose to upgrade an existing microscope with two high speed cameras for two color live imaging. A new laser source and a Spatial Light Modulator (SLM) will be added to the microscope to generate different speckle illuminations. Sophie Brustlein (CENTURI Multi-engineering platform) with some help from Simon Labouesse (postdoc in Thomas Lecuit’s team) will build the optical setup.
Finished projects
Applicant: Long-Fei Wu
Institute: LCB
Engineer: Sophie Brustlein & Mathias Lechelon
Submission date: 15/07/2020
Summary
Illumination with UV and violet light can change swimming velocity of multicellular bacteria in magnetic field. We need implement a custom-made microscope to determine the wavelength (energy) and irradiance (number of photons) require for triggering the photokinesis behavior.
Requested task
Need the help of optics and biophotonics engineer to modify the current design and construct the microscope, and mechatronics engineer to 3D print condenser and sample holders.
Applicant: Claire Valotteau
Institute: LAI
Engineer: Sophie Brustlein
Submission date: 23/10/2019
Summary
Acoustic Force Spectroscopy (AFS) is a newborn technique making use of acoustic pressure waves in a fluid channel to manipulate simultaneously hundreds tens of particles whose positions are tracked optically. We propose to use this tool to study the mechanical properties of cells. To do so, AFS will be used in compression mode, pushing the suspended cells against the surface of the fluid chamber. To determine the cell mechanical properties, the resulting deformation has to be precisely measured. Therefore, we suggest combining AFS with reflection interference contrast microscopy (RICM). RICM is an interferometric technique suited to visualize objects in the vicinity of a flat substrate. It is very well adapted for contact area analysis. Thus, the coupling of AFS and RICM will allow us to determine the cells viscoelastic properties, by applying known acoustic force and simultaneously measuring the resulting deformation on several cells in parallel.
Requested task
To achieve the goal described above, we need to implement a RICM setup on the optical microscope used for AFS. A new illumination source, appropriate filters, polarizer, analyzer, lambda quarter has to be selected, installed and properly aligned.
RICM observations are usually performed with oil immersion objectives. To optimize the coupling with AFS and avoid sound waves attenuation in oil, we would like to use air objectives. An objective benchmark would help to choose the best option while different coating options are brainstormed to reduce parasitic reflections on interfaces below and above the interface of interest.
Applicant: Mar Eroles Navarro
Institute: LAI
Engineer: Sophie Brustlein & Mathias Lechelon
Submission date: 15/09/2020
Summary
We want to implement on a existing optical microscope a new high throughput method called Deformation Cytometry to study cell mechanics. This method is based on microfluidics and requires both to implement a new sample holder and to use a high-speed camera to track optical deformation of cells under flow.
Requested task
A new sample holder has to be built to hold the microfluidic chip on the stage of the microscope (with the help of Matthias Lechelon).
In addition, a new high-speed camera has to be installed. Since the optical microscope is already being coupled to a camera for other application, a little optical module has to be built to enable the use of the second camera and a convenient switch from one system to the other. This module should also include a lens to enlarge the camera field of view.
Applicant: Pierre Szepetowski
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 15/10/2018
Summary
The project aims at evaluating the possible modulation of mTOR signaling pathway activity by NMDA receptors in living cells in vitro , using the appropriate mTORCAR FRET biosensor.
Requested task
Help of an optics/biophotonics engineer is needed to find the appropriate Imaging setup within the CENTURI community and train users to perform and optimize FRET experiments.
Applicant: Jorge Rodriguez Ramos
Institute: LAI
Engineer: Sophie Brustlein
Submission date: 23/10/2019
Summary
We are home-building our atomic force microscopy (AFM) head, coupled to a confocal spinning disk microscope to study biological samples (cells and tissues). The AFM will be coupled to a confocal spinning disk microscope to make simultaneous AFM and confocal studies.
Requested task
We need help with a group of tasks related to optics. On the one hand, the AFM head's development requires the alignment of the infrared laser system. On the other hand, the confocal system needs to be adapted to the new setup. We will also include an electrically tunable lens (ETL) in the optical path to automatize the sample focusing process.
Applicant: Julie Koenig Gambini
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 18/02/2020
Summary
My research project aims at understanding the role of entorhinal grid cells in spatial coding. These cells exhibited an increase in their firing rates in several regions of the environment arranged in a grid-like manner that tesselate the entire environment. A vast majority of computational models have proposed that grid cells rely mostly on self-motion information, in order to compute the distance travelled in comparison to a fixed point in the environment (distance coding). But, recent studies showed that grid cells are sensitive to contextual changes in external landmarks suggesting that they might be important to update the spatial representation of the environnent. Our goal is to dissect precisely the role of grid cells in distance coding and spatial representation.
Requested task
For this project, we want to record place cells in mice navigating in virtual environments during an inactivation of the medial septum. This inactivation is known to disrupt theta oscillations in the hippocampal formation and to specifically disrupt periodic firings of grid cells. Our goal is then to assess the impact of grid cells disruption on several aspects of spatial coding in the hippocampus. To do so, we would like to perfom optogenetics inactivation of the medial septum. Sophie's role will be to install the laser to perform such inactivation.
Applicant: Pierre-Pascal Lenck-Santini
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 20/09/2018
Summary
This project consists of building a set-up that drives a blue light beam at the proximity (50microns) of the recording sites of special electrodes called "sillicon probes". These electrodes have 4 shanks of 8 electrodes. Therefore the set-up will allow the experimenter to send light on one of the four shanks to induce firing of the neurons that are near the electrodes. The light is delivered via an optic fiber mounted on each electrode shank and be modulated via an analog signal (0-5V) sent by the experimenter.
Requested task
Advice on the best choice options for this project (ligh source, types of fibers, light modulator etc...), plan and design the apparatus, help to best align light sources and optic fibers.
Applicant: Sebastien Mailfert
Institute: CIML
Engineer: Sophie Brustlein
|
The super-resolution technique requires accurate correction for the mechanical motion of the sample and setup during acquisition. We aim at implementing a controller to actively stabilize the system during SMLM acquisition and consequently to reduce the drift across all three dimensions. Requested Task The engineer will help us to develop the optical part of the system based on an active three-dimensional real-time drift correction in collaboration with Sebastien Mailfert who will develop the optoelectronic part that will control the system. |
Applicant: Tom Borianne
Institute: CIML
Engineer: Sophie Brustlein
Submission date: 11/09/2020
Summary
Upon interaction with the peptide-Major Histocompatibility Complex (pMHC), the TCR rapidly shifts from an apparent homogeneous distribution to a dense cluster at the junction between a T cell and an antigen-presenting cell, termed the immunological synapse. It has been speculated that a remodeling of the plasma membrane organization mediates the signal transduction across the bilayer. Using a variety of solvatometric lipid probes, we would like to describe potential changes in the plasma membrane order inside TCR clusters and test what is the function of these changes in signal transduction.
Requested task
Our chemist collaborator Andrey Klymchenko in Strasbourg is sending us new probes that requiere 2-photon excitation. However, this probe can only be used on live cells and the current 2-photon microscope in the CIML is not adapted for such experiments (because it's not an inversed microscope so the objectives do no fit into small imaing chambers). Instead, we would like to use the 2-photon excitation of the ABLA microscope, currently non-fonctionnal.
Applicant: Alexandra Angelova
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 02/10/2020
Summary
The goal of our project is to investigate and manipulate the activity of mouse hippocampal neurons during a navigation task in a multisensory virtual reality. To this end we have built a 2-photon imaging set-up, coupled with a holographic stimulation pathway to specifically target the neurons of our interest in the living mouse.
Requested task
Our custom-made system needs some modifications in the major optical pathways in order to be stable and fully functional.
Applicant: Mathieu Fallet
Institute: CIML
Engineer: Sophie Brustlein
Submission date: 10/11/2020
Summary
The purpose of the project with Rejane Rua is to do intravital imaging in multicolors (SHG, vessels, macrophage in GFP) to visualize the traffic of macrophages in meninges of slept mouse. Myelin can be also interesting to visualize :
"Multiple sclerosis is a widespread debilitating autoimmune disease with no efficient treatment available. During the disease process, autoreactive lymphocytes attack the central nervous system (CNS), which leads to alteration of the blood-brain barrier integrity, myelin degradation and impairment of neuronal functions. Using mouse models, we found that in the meninges that surround the CNS, inflammation can be detected even before the onset of the disease, and is the best predictor of parenchymal inflammation. "
Requested task
The two photon microscope in CIML is equipped with an OPO that need to be realigned (it was not used during 4 years). The main laser need also to be realigned with the OPO light temporally and spatially to obtain a non linear contrast names CARS able to excite CH bond rich in lipids regions like myelin in neurone that is interesting to monitor.
The intravital imaging is never an easy technic that ask many adaptations that Sophie could provide due to her large experience in this field to begin and follow this kind of experience.
Applicant: Rémi Lasserre
Institute: CIML
Engineer: Sophie Brustlein
Submission date: 12/02/2021
Summary
This project consists in developping an optic device adapted to our microscope, designed to shape the illumination of a LED system to produce patterned cell photostimulations.
Requested task
- design of a cost effective strategy to shape the light coming from a specific LED source.
- building and evaluate the device
Applicant: Tom Borianne
Institute: CIML
Engineer: Sophie Brustlein
Submission date: 01/03/2021
Summary
The project aims to use STED super-resolution to conduct solvatometric imaging of T cell plasma membrane during immune synapse formation. The gain of spatial resolution should allow to descriminate the plasma membrane from the endoplasmic reticulum, which are in close proximity in primary T cells.
Requested task
The STED microscope requires a re-alignement of the optical path of the STED depletion beam.
Applicant: François Michel
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 22/12/2022
Summary
Analysis of the developmental scaffold of the hippocampus
Requested task
We have a Trimscope specifically dedicated to in vitro calcium imaging that need to be re-construct with new pieces.
Applicant: Mathieu Fallet
Institute: CIML
Engineer: Sophie Brustlein
Submission date: 22/12/2022
Summary
The project consist to develop an optical bench to characterize objective aberrations (Strehl ratio and Zernike coefficient) using a phase camera (Shak-Hartmann).
The camera was financed by the RT-mfm (Pierre Bon) in the beginning of 2021.
The optical bench could be used by other institute in France for objective characterization (collaboration with Orestis Faklaris) in Montpellier.
Requested task
Set-up a first development with low numerical aperture objective (10x) as a proof of principle on an optical board using optics from CIML (laser, condenser, mirror, pinhole, XY stage, density filter and telescope).
Further development could be done to integrate the wavefront sensor directly on microscope (after the C mount of the microscope for instance)
Applicant: Julie Koenig Gambini
Institute: INMED
Engineer: Sophie Brustlein
Submission date: 22/12/2022
Summary
My research project aims at understanding the role of entorhinal grid cells in spatial coding. These cells exhibited an increase in their firing rates in several regions of the environment arranged in a grid-like manner that tesselate the entire environment. A vast majority of computational models have proposed that grid cells rely mostly on self-motion information, in order to compute the distance travelled in comparison to a fixed point in the environment (distance coding). But, recent studies showed that grid cells are sensitive to contextual changes in external landmarks suggesting that they might be important to update the spatial representation of the environnent. Our goal is to dissect precisely the role of grid cells in distance coding and spatial representation.
Requested task
For this project, we want to record place cells in mice navigating in virtual environments during an inactivation of the medial septum. This inactivation is known to disrupt theta oscillations in the hippocampal formation and to specifically disrupt periodic firings of grid cells. Our goal is then to assess the impact of grid cells disruption on several aspects of spatial coding in the hippocampus. To do so, we would like to perfom optogenetics inactivation of the medial septum. Sophie's role will be to install the laser to perform such inactivation.
Applicant: Long-Fei Wu
Institute: LCB
Engineer: Sophie Brustlein & Mathias Lechelon
Submission date: 06/10/2020
Summary
We have isolated marine bacteria of which the growth is boosted by infrared. We wish to monitor the growth and absorption of the cultures on real time.
Requested task
Design and construct, together with Sophie Brustlein, a illumination system that allow measuring growth and light absorption on real time.
Applicant: Emmanuèle Helfer
Institute: CINaM
Engineer: Sophie Brustlein
The project requires the help of an engineer in optics for finalizing the implementation of an optical tweezers experiment. The setup consists in focusing an infrared (IR) laser in the sample via the microscope objective, the laser beam will be deviated by acousto-optic deflectors (AODs) at the back focal plane of the objective, leading to a translation of the optical trap in the focal plane. AODs allow fast switch between several positions thus simultaneous trapping of multiple objects.
The experiment will be used for several projects in the group: 1) to apply forces on single cells and nuclei and measure their mechanical properties, in the frame of premature aging diseases (nuclei with altered mechanics); 2) to pull membrane tubules from artificial vesicles and determine conditions required for tube fission. The setup can be used by CENTURI colleagues for other projects, for example to investigate flows generated by coordinated cilia cells.
Keywords: optical tweezers, microscopy, acousto-optic deflectors, mechanical stress/strain
Applicant: Didier Marguet
Institute: CIML
Engineer: A. Mengistie Taddese
Summary
For the EU LINkS project, it is necessary to record molecular diffusions and at the same time create the experimental conditions to generate long-range electrodynamic intermolecular forces by pumping the sample with a different light source than the one used for FCS measurements.
The setup requires the design of two different light paths, one for confocal and one for wide-field excitation, for FCS and LEDI pumping force, respectively.
Requested task
We request the expertise of the CENTURI engineer in charge of the optical development. He will build the system and align the optical bench, based on the plan already established in collaboration with Sophie Brustlein. He will have to adapt or design mechanical parts of the designed setup to adjust the lasers, sample holder, Z piezo on the XY motorized stage, etc.
Sébastien Mailfert (CIML) will help him in the optoelectronic aspect of the project. Together, they will validate the system.
NEUROSCIENCE & DATA ANALYTICS
Finished projects
Applicant: Rosa Cossart
Institute: INMED
Engineer: Stefania Sarno
Submission date: 14/09/2021
Project summary :
The hippocampus is classically described as providing a cognitive map of space and time, underlying navigation, learning, and memory. To serve these functions, hippocampal circuits produce sequences of neuronal activation arising from the interaction between external inputs and internally-generated preconfigured dynamics. The developmental timeline for the emergence of hippocampal sequences remains unknown partly due to the lack of statistical methods allowing for their unbiased detection . The aim of this project is to develop tools allowing for the analysis of sequential activity from calcium imaging datasets as described in Villette et al (2015).
Requested task :
Develop a statistical method to validate the detection of sequences.
Applicant: Elodie Fino
Institute: INMED
Engineer: Stefania Sarno
Submission date: 24/01/2022
Project summary :
‘It’s like riding a bike!’. But what does that look like in the brain? By combining modulation of neural circuits with an accelerating rotating rod task in mice (A) and deep neural networks (B), we want to better understand how motor learning develops, and becomes habitual with practice. We use behavioral tracking of mice trained on the rotarod with the open source software DeepLabCut and extract datapoints of different bodyparts throughout the training.
Requested task :
The idea will be to develop algorithms to organize all the data points from the time series (x and y coordinates of body markers provided by DLC tracking), eliminate artifacts and detect a number of different patterns in the trajectories of the different markers, as the mice become better at walking on the rotating rod. Also, quantifying and clustering single mouse behavior over time, comparing different mice behaviors and classify them according to the type of patterns. Finally, determine whether specific patterns are predictable.
Applicant: Jérôme Laurin
Institute: INMED
Engineer: Stefania Sarno
Submission date: 08/01/2022
Project summary :
The purpose of the project is to first define effects of exercise intensity and the training effect on the prefrontal cortex activity in adolescent rats and to show the effect of KCC2 (chloride homeostasis co-transporter) on neuronal activity and neurotrophic factors expression in training conditions. By using the Inscopix device, we'll record the in vivo calcium imaging during incremental exercise test and training session on treadmill to define the time course of brain activity changes depending on the type of training regimen.
Requested task :
It seems important to involve an engineer to drive the data analysis of the calcium imaging in the prefrontal cortex. We should see together the possibilities in terms of recorded parameters we can extract from the signal.
Applicant: David Robbe
Institute: INMED
Engineer: Stefania Sarno
Submission date: 03/03/2022
Project summary :
Recent works have shown how crucial it is for neuroscience to finely characterize animal behaviour. In our Lab we are mainly interested in two aspects of behavioural analysis:
First, characterize how animals adapt their decisions based on received rewards, and how their behavioural strategy evolves during learning. Second, understand how animals tradeoff their willingness to receive rewards as soon as possible with the effort that is required to approach reward fast (known as the time/effort trade off).
Unveiling statistical structure in massive behavioural data requires machine learning and deep learning techniques. Further interpretability of the results would ideally require the usage of simple optimal control/ reinforcement learning techniques, to perform appropriate model fitting.
Requested task :
Develop a statistical method to understand how behavior evolves over time during task learning. The data are the trajectory of animals on a trial-by-trial and session-by-session basis. The methods are related to machine learning and dimensionality reduction.
Applicant: Jérôme Epsztein
Institute: INMED
Engineer: Stefania Sarno
Submission date: 17/11/2021
Summary
Our project aim at understanding the mechanisms of self location and spatial memory in young and adult mice and how it is altered in several pathological conditions. We use intracranial electrodes to record brain activity in parts of the brain that are important for self location and memory. In the furture we would like to use electrodes with increasing recording sites and need to adapt our data processing pipeline to this technical evolution.
Requested task
We would like the help of an engineer to upgrade our data processing pipeline using newly developed softwares and toolboxes compatible with the use of high density probes (e.g. kilosort, spyking circus, tridesclous, spike interface for neuropixel probes) and interface it with our current data analysis pipeline.
Applicant: Laurent Aniksztejn
Institute: INMED
Engineer: Stefania Sarno
Submission date: 07/02/2022
Summary
Developmental and Epileptic encephalopathies (DEEs) represent a heterogeneous group of mostly neonatal, infantile and childhood-onset disorders that associate severe epilepsy with a rapid deterioration of cognitive/sensory and motor functions. There is a genetic basis for DEEs. Notably, de novo mutations of KCNQ2 encoding the Kv7.2 subunit of the potassium Kv7/M channel are shown to be the most frequently genetic cause of neonatal-onset DEE but the underlying pathophysiological mechanism remains poorly known. We currently study a knock-in mouse model carrying the recurrent p.T274M variant to better understand how a given Kv7.2 pathogenic variant alters cortical network functioning and ultimately at designing pharmacological options. For this purpose we will investigate both in vivo and ex-vivo in neocortical slices and using patch-clamp technique the electrophysiological consequences that the variant may have on neuronal excitability, Kv7 channels function and network activity.
Requested task
We want to compare neuronal excitability in wild-type cells, mutant cells and wild-type cells treated with a Kv7 channel blocker. We need help for performing appropriate statistical analysis. The analysis will require the use of the software R.
Applicant: Valery Matarazzo
Institute: INMED
Engineer: Stefania Sarno
Submission date: 11/04/2023
Project summary :
Atypical responses to sensory stimuli are considered as a core aspect and early life marker of Autism Spectrum Disorders (ASD). Our research concentrates on neonate mice lacking the autism-associated gene Magel2 and our previous results suggest a dysfunction in neural coding of thermoception that we need now to investigate. By recording thermal cortical evoked potentials through in vivo electrophysiological multi-channel recording we aim to 1) identify the existence of early activity in the somatosensory cortex induced by cool thermal stimulation; 2) Compare cortical activity between control and Magel2 deficient mice.
Requested task :
Conversion of XDAT to DAT files
Spyke sorting analyses
Frequence analyses of LFP
Figures.