BIO-IMAGE ANALYSIS
The Necker Bio-image Analysis Platform provides software tools (both open-source
and licensed), advanced analysis workstations compatible with machine learning,
and expertise in image analysis and related fields to deliver technological
and methodological solutions.
The platform offers personalized support throughout the analysis of biological data generated from a wide range of imaging modalities (light microscopy, electron microscopy, histology, medical imaging, etc.). This support is always provided in close scientific collaboration with users and other relevant core facilities.
The platform is available to research teams on the Necker campus and is fully open
to external partners from both the public and private sectors.
SERVICES
MISSIONS
Bioimage analysis has been organized as a support service for research teams, structured around four main missions:
ADVISE
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Providing guidance and support to researchers regarding image analysis possibilities before, during, and after a project. Discussing results and assisting with manuscript writing and publication review..
ANALYZE
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Designing and documenting image analysis protocols tailored to the specific needs
of research teams.
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Developing scripts to automate analyses and supporting users in their implementation.
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Providing access to high-performance analysis workstations, remotely accessible, adapted to analytical requirements, and compatible with machine learning approaches.
TRAIN
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Training researchers in the use of open-source and licensed image analysis software.
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Creating video tutorials to facilitate knowledge transfer within laboratories.
DEVELOP
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Designing, in collaboration with researchers, new analytical approaches to address specific needs, such as the reuse of published plugins, artificial intelligence-based methods, and more.
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Training deep learning neural networks for the development and improvement
of 2D image analysis models.
EXPERTISE
The platform provides expertise in:
EXPERIMENTAL DESIGN
Assisting in the development of experimental plans at the beginning of projects,
focusing on critical factors for optimal image analysis (labeling strategies, image quality
and resolution, etc.).
COMPLEX IMAGE ANALYSIS WORKFLOW
Designing complex image analysis protocols, from preprocessing to result synthesis, involving multiple processing steps and software tools.
AUTOMATION
Developing manual, semi-automated, and automated methods (using scripts and macros) for identifying structures in 2D, 3D (volumetric or 2D + time), and 4D (3D + time) datasets.
QUANTITATIVE MEASUREMENTS
Performing measurements of identified structures using various analytical techniques, including:
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2D/3D skeletonization for measuring length, tortuosity, branching, and related parameters, commonly used in vascular biology, primary cilia research,
and neuroscience.
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Colocalization analysis to study interactions between biological targets.
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Tracking analysis for monitoring dynamic events over time.
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Distance measurements between objects, enabling assessments of density, relocalization/delocalization phenomena, and spatial organization within images.
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Morphological analysis of 2D and 3D structures.
ARTIFICIAL INTELLIGENCE AND MACHINE LEARNING
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Shallow Learning approaches using algorithms for pixel classification and object classification model training.
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Deep Learning approaches using neural networks for both the application
of pretrained models (inference) and the training of new models.
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Quality control and validation of prediction results to ensure the reliability
of developed models.
DATA INTERPRETATION AND KNOWLEDGE TRANSFER
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Assisting with the interpretation of analysis results.
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Facilitating protocol dissemination through comprehensive documentation and video tutorials highly appreciated by research teams.
EQUIPMENTS
All analysis workstations are compatible with artificial intelligence tools.
The following open-source software packages are installed on all systems :
FIJI, Ilastik, QuPath, Icy, CellProfiler.
The following open-source neural network tools for 2D segmentation are also available
on all workstations: 2D StarDist (FIJI/QuPath), Cellpose3 et CellposeSAM (FIJI/QuPath), SAM (QuPath/FIJI) et InstanSeg (QuPath).
In addition, the licensed software packages Imaris and Arivis provide advanced analysis solutions, including machine learning capabilities (both shallow learning and deep learning), for 3D and 4D imaging datasets and large-scale datasets exceeding 100 GB.
ANALYSIS ROOM – FACULTY OF MEDICINE BUILDING
(1st floor room 108b)
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1 Analysis Workstation with licenced software : Imaris latest version
(Intel 20core / 128Go RAM / 2x SSD 4 to Go + HDD 6To / GPU Nvidia 16 Go)
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1 Analysis Workstation with licenced software : ArivsPro latest version
(Intel 12core - 24threads / 128Go RAM / 4 SSD nvme 4To + HDD 10 To / GPU Nvidia 48 Go)
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1 Analysis Workstation dedicated to opens source and AI
(Intel 12core - 24threads / 128Go RAM / SSD 512 go + HDD 5To / GPU Nvidia 12 Go)
IMAGINE BUIDING
(2d floor near room 208)
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1 Analysis Workstation with licenced software : Imaris v9.5.3
(Intel 20core - 40threads / 128Go RAM / SSD 512 Go + 2x HDD 2 To / GPU Nvidia 8Go)
EXAMPLES
The platform has a varied panel of analyses but it is also possible to develop,
in collaboration with the research teams, new approaches which are not yet included
in the portfolio.
Some examples below:
SEGMENTATION
Filaments like structure:
Primary cilia: Length and straightness measurements
Credit: Damelys Calderon
Spots like structure
number of spots per cell
Rossignol et al.- Neuropilin-1 cooperates with PD-1
in CD8 + T cells predicting outcomes in melanoma patients treated with anti-PD1 -
iScience 25,104353 June 17, 2022
Cell–like structure
Kaimal, Jay, & Thul, Peter. (2021). HPA Cell Image Segmentation Dataset (Version v2) [Data set]. Zenodo
Bacteria–like structure
Credit: omnipose GUI
Complex tissular structure
3D Nephron, cysts and vascular system if kidneys
T Blanc et al. - Three-dimensional architecture of nephrons in the normal and cystic kidney -
Kidney International (2021) 99, 632–645
COLOCALIZATION MEASUREMENT
By area (2D) and volume (3D) overlay
L. Cheradame et al. - STING protects breast cancer cells from intrinsic and genotoxic-induced DNA instability via a non-canonical, cell-autonomous pathway - Oncogene (2021) 40:6627 – 6640
DISTANCE ANALYSIS 3D/2D
Counting spots inside mitochondria
Credit: Eloïse Marques
Counting cells inside and at a certain distance of a delimitate tissular structure
Credit: Florence Vasseur
MEASUREMENTS
Volume / Area
Adipocytes area of a tissular structure
Ladraa et al. - PIK3CA gain-of-function mutation in adipose tissue induces metabolic reprogramming with Warburg-like effect and severe endocrine disruption - Sci. Adv. 8, eade7823 (2022)
Counting
number of foci per nuclei
L. Cheradame et al. - STING protects breast cancer cells from intrinsic and genotoxic-induced DNA instability via a non-canonical, cell-autonomous pathway - Oncogene (2021) 40:6627 – 6640
Intensity measurments
P. Renard et al. - Hydroxychloroquine sulfate: A novel treatment for lipin-1 deficiency? - Biomedicine & Pharmacotherapy 163 (2023) 114813
Morphological measurements
Bernheim et al. - Identification of Greb1l as a genetic determinant of crisscross heart in mice showing torsion
of the heart tube by shortage of progenitor cells- 2023, Developmental Cell 58, 2217–2234
OBJECT CLASSIFICATION
3D mitochondries segmentation and classification
E. Cosialls et al. - mTOR inhibition suppresses salinomycin-induced ferroptosis in breast cancer stem cells
by ironing out mitochondrial dysfunctions – Springer Nature Cell Death and Disease (2023) 14:744
TIME LAPSE ANALYSIS
Dynamic events
counting spots at different time point
I.Munoz et al. -Kinesin-1 regulates mast cell degranulation - JCB • Volume 215 • NumBer 2 • 2016
Tracking
measurements along time (speed, area, displacement, etc.)
Credit: Iwona Pranke
CREATION / IMPROVEMENT OF A 2D DEEPLEARNING MODEL
Credit: Thierry Capiaud
STAFF
Nicolas GOUDIN
Head
Pablo VARGAS
Scientific Referent
SCIENTIFIC STEERING COMMITTEE
IMAGINE
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Sophie Thomas, PhD ; sophie.thomas@inserm.fr
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Audrey Desgrange, PhD ; audrey.desgrange@institutimagine.org
INEM
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Etienne Morel, PhD ; etienne.morel@inserm.fr
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Julien Diana, PhD ; julien.diana@inserm.fr
BIGR
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Bérengère Koehl, MD, PhD ; berengere.koehl@aphp.fr
FEES
For any pricing indication, please contact the platform at this address : nicolas.goudin@inserm.fr
PUBLICATIONS
Mitochondrial dynamics and metabolic regulation control T cell fate in the thymus.
Elhage R, Kelly M, Goudin N, Megret J, Legrand A, Nemazanyy I, Patitucci C, Quellec V, Wai T, Hamaï A, Ezine S. Front Immunol. 2024 Jan 15;14:1270268. doi: 10.3389/fimmu.2023.1270268. eCollection 2023. PMID: 38288115
The AMPK-Sirtuin 1-YAP axis is regulated by fluid flow intensity and controls autophagy flux in kidney epithelial cells.
Claude-Taupin A, Isnard P, Bagattin A, Kuperwasser N, Roccio F, Ruscica B, Goudin N, Garfa-Traoré M, Regnier A, Turinsky L, Burtin M, Foretz M, Pontoglio M, Morel E, Viollet B, Terzi F, Codogno P, Dupont N. Nat Commun. 2023 Dec 5;14(1):8056. doi: 10.1038/s41467-023-43775-1. PMID: 38052799
Hemifacial myohyperplasia is due to somatic muscular PIK3CA gain-of-function mutations and responds to pharmacological inhibition.
Bayard C, Segna E, Taverne M, Fraissenon A, Hennocq Q, Periou B, Zerbib L, Ladraa S, Chapelle C, Hoguin C, Kaltenbach S, Villarese P, Asnafi V, Broissand C, Nemazanyy I, Autret G, Goudin N, Legendre C, Authier FJ, Viel T, Tavitian B, Gitiaux C, Fraitag S, Duong JP, Delcros C, Sergent B, Picard A, Dussiot M, Guibaud L, Khonsari R, Canaud G. J Exp Med. 2023 Nov 6;220(11):e20230926. doi: 10.1084/jem.20230926. Epub 2023 Sep 15. PMID: 37712948
Hydroxychloroquine sulfate: A novel treatment for lipin-1 deficiency?
Renard P, Caccavelli L, Legendre A, Tuchmann-Durand C, Balakirouchenane D, Blanchet B, Narjoz C, Straube M, Hubas A, Garros A, Mention K, Bednarek N, Goudin N, Broissand C, Schlatter J, Cisternino S, Cagnard N, van Endert P, Diana J, de Calbiac H, de Lonlay P. Biomed Pharmacother. 2023 Jul;163:114813. doi: 10.1016/j.biopha.2023.114813. Epub 2023 May 5. PMID: 37150031
DOCK11 deficiency in patients with X-linked actinopathy and autoimmunity.
Boussard C, Delage L, Gajardo T, Kauskot A, Batignes M, Goudin N, Stolzenberg MC, Brunaud C, Panikulam P, Riller Q, Moya-Nilges M, Solarz J, Repérant C, Durel B, Bordet JC, Pellé O, Lebreton C, Magérus A, Pirabakaran V, Vargas P, Dupichaud S, Jeanpierre M, Vinit A, Zarhrate M, Masson C, Aladjidi N, Arkwright PD, Bader-Meunier B, Baron Joly S, Benadiba J, Bernard E, Berrebi D, Bodemer C, Castelle M, Charbit-Henrion F, Chbihi M, Debray A, Drabent P, Fraitag S, Hié M, Landman-Parker J, Lhermitte L, Moshous D, Rohrlich P, Ruemmele F, Welfringer-Morin A, Tusseau M, Belot A, Cerf-Bensussan N, Roelens M, Picard C, Neven B, Fischer A, Callebaut I, Ménager M, Sepulveda FE, Adam F, Rieux-Laucat F. Blood. 2023 Jun 1;141(22):2713-2726. doi: 10.1182/blood.2022018486. PMID: 36952639
PIK3CA gain-of-function mutation in adipose tissue induces metabolic reprogramming with Warburg-like effect and severe endocrine disruption.
Ladraa S, Zerbib L, Bayard C, Fraissenon A, Venot Q, Morin G, Garneau AP, Isnard P, Chapelle C, Hoguin C, Fraitag S, Duong JP, Guibaud L, Besançon A, Kaltenbach S, Villarese P, Asnafi V, Broissand C, Goudin N, Dussiot M, Nemazanyy I, Viel T, Autret G, Cruciani-Guglielmacci C, Denom J, Bruneau J, Tavitian B, Legendre C, Dairou J, Lacorte JM, Levy P, Pende M, Polak M, Canaud G. Sci Adv. 2022 Dec 9;8(49):eade7823. doi: 10.1126/sciadv.ade7823. Epub 2022 Dec 9. PMID: 36490341
Neuropilin-1 cooperates with PD-1 in CD8+ T cells predicting outcomes in melanoma patients treated with anti-PD1.
Rossignol J, Belaid Z, Fouquet G, Guillem F, Rignault R, Milpied P, Renand A, Coman T, D'Aveni M, Dussiot M, Colin E, Levy J, Carvalho C, Goudin N, Cagnard N, Côté F, Babdor J, Bhukhai K, Polivka L, Bigorgne AE, Halse H, Marabelle A, Mouraud S, Lepelletier Y, Maciel TT, Rubio MT, Heron D, Robert C, Girault I, Lebeherec D, Scoazec JY, Moura I, Condon L, Weimershaus M, Pages F, Davoust J, Gross D, Hermine O. iScience. 2022 May 5;25(6):104353. doi: 10.1016/j.isci.2022.104353. eCollection 2022 Jun 17. PMID: 35874918
The critical role of the TB5 domain of fibrillin-1 in endochondral ossification.
Delhon L, Mougin Z, Jonquet J, Bibimbou A, Dubail J, Bou-Chaaya C, Goudin N, Le Goff W, Boileau C, Cormier-Daire V, Le Goff C. Hum Mol Genet. 2022 Nov 10;31(22):3777-3788. doi: 10.1093/hmg/ddac131. PMID: 3566086
2D and 3D Human Induced Pluripotent Stem Cell-Based Models to Dissect Primary Cilium Involvement during Neocortical Development.
Boutaud L, Michael M, Banal C, Calderon D, Farcy S, Pernelle J, Goudin N, Maillard C, Dimartino C, Deleschaux C, Dupichaud S, Lebreton C, Saunier S, Attié-Bitach T, Bahi-Buisson N, Lefort N, Thomas S. J Vis Exp. 2022 Mar 25;(181). doi: 10.3791/62667. PMID: 35389978
STING protects breast cancer cells from intrinsic and genotoxic-induced DNA instability via a non-canonical, cell-autonomous pathway.
Cheradame L, Guerrera IC, Gaston J, Schmitt A, Jung V, Goudin N, Pouillard M, Radosevic-Robin N, Modesti M, Judde JG, Cairo S, Goffin V. Oncogene. 2021 Dec;40(49):6627-6640. doi: 10.1038/s41388-021-02037-4. Epub 2021 Oct 8. PMID: 34625708