Presentation
The Necker Bio-image Analysis platform has been created to answer the two institutes images analysis needs in the service of bio-images treatment and analysis.
Its perimeter includes all imaging modalities coming from:
i) platforms (like the microscopy and the histology),
ii) common resources from the 2 institutes (Incucytes, etc.),
or iii) Research team systems of Necker Campus or outside.
All platform work is performed in a scientific collaboration with the users and the concerned platforms.
What is “image analysis” ?
"In biology, image analysis is a process of identifying spatial distribution of biological components in images and measuring their characteristics to study their underlying mechanisms in an unbiased way" (2016) Bioimage Data Analysis.
Here are the main steps :
Sample preparation, imaging modalities choice, acquisition parameters, all will have an influence on the image analysis and its results. So it is important to prepare your scientific project and the biological hypothesis you want to prove according to this image analysis (“what I want to highlight, and how to reach it”).
PROPOSED SERVICES
- Advice and support on image analysis possibilities
- Training on place or in videoconference on the basic use of analysis software : open-source (Fiji, Icy, Ilastik, QuPath, etc.) and under licenses (Huygens, Imaris, Calopix, etc.).
- Creation and redaction of specific analysis workflow
- Open-source software macro writing for to automate your analysis and support in their comprehension to reuse it.
- Script writing for Excel results compilation and support in their comprehension to reuse it
1. The Necker Bio-image Analysis platform is available for consultative meetings at every steps of the project.
2. For every image analysis project :
A first meeting will be plane for an images visualisation and then decide of the analysis feasibility.
In the case where the analysis center cannot satisfy the wished analysis (lack of data, too much altered image, etc.), a detailed report of the disturbing analysis point will be give and other analysis strategies will be proposed.
3. Once the workflow was established :
A report containing all the analysis steps (from pre-treatment to results extraction and synthesis), the software used and the analysis key points, that can be source of possible bias will be given to the user.
On demand, a complete analysis folder (raw images used to make the workflow and the scripts, images coming for the different workflow’s steps and the results obtains by the workflow) could be given to the user.
Localisation
Office : Fac building Rdc R24 - Tel : +33 (0)1.40.61.55.48
Analysis room : Faculté de Médecine building: 1 rst floor room 108b
Analysis room IMAGINE building : 2 nd floor (close to door 208)
Staff
Equipement
The open-source analysis software Fiji, Icy, Ilastik and Qupath are installed on all analysis systems
Faculty building
1st floor room 108b :
-
1 workstation
CPUs AMD 24 cœurs - 48 threads / 128 Go de RAM / 12 To de stockage / GPU Nvidia 8 Go
-
1 analysis system with Imaris v9.5.3
CPUs Intel 6 cœurs - 12 threads / 24 Go de RAM / 5 To de stockage / GPU Ati 1 Go
IMAGINE building
2d floor (close to door n°208) :
-
1 workstation with Imaris and Imaris stitcher v9.6
CPUs Intel 12 core - 24 threads / 128 Go de RAM / 5 To for storage/ GPU Ati 3 Go
-
1 workstation with Huygens
CPUs Intel 20 core-40 threads/128Go de RAM / 2x 2 To for storage/GPU Nvidia 8Go
-
1 analysis system
CPUs Intel 4 core - 8 threads / 32 Go de RAM / 2 To for storage/ GPU Nvidia 2 Go
floor -1 room S10:
-
1 analysis system for the histology slide scanner images recovery
Fees
For year 2021, year of the implementation of the image analysis center, there is no Fees, The fees will be calculated starting from January 2022.
Publications
Blanc T, Goudin N, Zaidan M, Traore MG, Bienaime F, Turinsky L, Garbay S, Nguyen C, Burtin M, Friedlander G, Terzi F, Pontoglio M. Three-dimensional architecture of nephrons in the normal and cystic kidney. Kidney Int. 2021 Mar;99(3):632-645.
Guillem F, Dussiot M, Colin E, Suriyun T, Arlet JB, Goudin N, Marcion G, Seigneuric R, Causse S, Gonin P, Gastou M, Deloger M, Rossignol J, Lamarque M, Choucair ZB, Gautier EF, Ducamp S, Vandekerckhove J, Moura IC, Maciel TT, Garrido C, An X, Mayeux P, Mohandas N, Courtois G, Hermine O. XPO1 regulates erythroid differentiation and is a new target for the treatment of β-thalassemia. Haematologica. 2020 Sep 1;105(9):2240-2249.
Le TL, Sribudiani Y, Dong X, Huber C, Kois C, Baujat G, Gordon CT, Mayne V, Galmiche L, Serre V, Goudin N, Zarhrate M, Bole-Feysot C, Masson C, Nitschké P, Verheijen FW, Pais L, Pelet A, Sadedin S, Pugh JA, Shur N, White SM, El Chehadeh S, Christodoulou J, Cormier-Daire V, Hofstra RMW, Lyonnet S, Tan TY, Attié- Bitach T, Kerstjens-Frederikse WS, Amiel J, Thomas S. Bi-allelic Variations of SMO in Humans Cause a Broad Spectrum of Developmental Anomalies Due to Abnormal Hedgehog Signaling. Am J Hum Genet. 2020 Jun 4;106(6):779-792.
Belabed M, Mauvais FX, Maschalidi S, Kurowska M, Goudin N, Huang JD, Fischer A, de Saint Basile G, van Endert P, Sepulveda FE, Ménasché G. Kinesin-1 regulates antigen cross-presentation through the scission of tubulations from early endosomes in dendritic cells. Nat Commun. 2020 Apr 14;11(1):1817.