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INSTITUT COCHIN ENTITY DMP - IMAG'IC Core
Facility

Pierre Bourdoncle, Thomas Guilbert

► To cite this version:

Pierre Bourdoncle, Thomas Guilbert. INSTITUT COCHIN ENTITY DMP - IMAG'IC Core Facility. Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Cité, F-75014 Paris, France. 2024, https://institutcochin.fr/plateformes/imagic. hal-04834141v2

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Submitted on 18 Dec 2024

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# INSTITUT COCHIN ENTITY DMP - IMAG'IC

Plan de gestion de données créé à l'aide de DMP OPIDoR, basé sur le modèle "Science Europe: structured template for research entities" fourni par DMP OPIDoR.

## Plan Details

**Plan title** INSTITUT COCHIN ENTITY DMP - IMAG'IC

**Deliverable**

**Version** First version

**Plan purpose/scope** The aim of this DMP is to describe as precisely as possible the various research products produced by the services offered by the core facility. This DMP is part of a wider framework, that of making available all the DMPs of the 9 Institut Cochin core facilities (MOUSET'IC, PROTEOM'IC, PIV, PIME, METABOL'IC, CYBIO, IMAG'IC, GENOM'IC and HISTIM) as well as the DMP of the CID database dedicated to the transfer, storage, consultation and sometimes processing of most of the data produced by the Institut Cochin's core facilities. The purpose of this DMP entity is to provide drafting assistance for researchers wishing to draw up a DMP for their research projects and wishing to call on the expertise of our core facilities.

**Fields of science and technology (from OECD classification)** 1.6 Biological sciences

**Language** eng

**Creation date** 2024-07-04

**Last modification date** 2024-12-18

**Identifier** https://doi.org/10.57889/imag_ic Cf

**Identifier type** DOI

**License**

**Name** Creative Commons Attribution 4.0 International

**URL** http://spdx.org/licenses/CC-BY-4.0.json

## Structure Details
<table><tr><td>Entity's name</td><td>Institut Cochin Core Facility - IMAG'IC</td></tr><tr><td>Acronym</td><td>IMAG'IC</td></tr><tr><td>Identifier</td><td>https://institutcochin.fr/plateformes/imagic</td></tr><tr><td>Identifier type</td><td>URL</td></tr><tr><td>Description</td><td>The IMAG'IC cellular imaging core facility at the Institut Cochin is part of the France BioImaging national infrastructure. Spread over 130 m² in the heart of Paris, it has 15 acquisition systems: widefield, confocal, super-resolution (PALM, STORM, STED), multiphoton (spectral, intra-vital, SHG, FLIM), TIRF, FRET-FLIM, flow imaging, etc. It is also equipped with 3 image analysis and processing stations.<br> Anyone working in a public or private laboratory can benefit from assistance or training to become autonomous on the platform's microscopes. IMAG'IC also offers image restoration services using 3D deconvolution, a database (Cochin Image Database), 3D printing, thick tissue sections using the vibratome and tissue clarification.<br> IMAG'IC is an open-access collaborative facility enabling researchers from within Institut Cochin and elsewhere to perform cutting-edge studies using state-of-the-art equipment. This includes research on diverse samples like cells or tissues, both in vitro and in vivo. Many of the instruments are located in biosafety levels 2 and 3 laboratories, which allows imaging of live cells, tissue samples of human origin and/or infected with pathogens, and whole mammals infected with communicable diseases.<br> All our systems are accessible via a CID image database for backup, archiving, processing, analysis & sharing.<br> We are very attached to our different networks which are an inexhaustible source of useful knowledge for our businesses, locally (RTmfm, GDR Imabio -MiFoBio & France-BioImaging) and internationally (QUAREP-LiMi & EuroBioImaging).</td></tr><tr><td>Creation date</td><td>2000-01-01</td></tr></table>

**Research outputs :**

1. Light microscopy images (Image)

2. Biological Samples (Physical object)

3. Image processing softwares (Software)

**Contributors**
<table><thead><tr><td>Name</td><td>Affiliation</td><td>Roles</td></tr></thead><tbody><tr><td>Bourdoncle Pierre - 0009-0005-0868-363X</td><td>Institut Cochin - 051sk4035</td><td><ul><li>Data Collector (Images, Softwares, Softwares)</li><li>Entity's Manager (Images, Images, Images, Images, Images, Images, Images, Images, Softwares, Samples, Softwares, Softwares, Softwares, Softwares, Images)</li><li>Entity's manager</li></ul></td></tr><tr><td>Braud-Mussi Raphaël - https://institutcochin.fr/annuary/raphael-braud-mussi</td><td>Institut Cochin - 051sk4035</td><td><ul><li>Data Collector (Softwares, Images, Softwares)</li></ul></td></tr><tr><td>Guilbert Thomas - 0000-0001-5069-0730</td><td>Institut Cochin - 051sk4035</td><td><ul><li>DMP manager</li><li>Data Collector (Softwares, Images, Images)</li></ul></td></tr><tr><td>Le Goff Gabriel</td><td>Institut Cochin - 051sk4035</td><td><ul><li>Contact Person (Softwares)</li><li>Data Collector (Images, Softwares, Softwares, Images)</li></ul></td></tr><tr><td>Lesieur Julie</td><td>Institut Cochin - 051sk4035</td><td><ul><li>Contact Person (Samples)</li><li>Data Collector (Samples, Samples, Samples, Samples, Images)</li></ul></td></tr></tbody></table>
Data description and collection or re-use of existing data

Light microscopy images

Research output description

Name Light microscopy images

Description The IMAG'IC photonic microscopy core facility provides users with around fifteen microscopes that generate images in different formats and of varying dimensions. These images are used by the biology community for fundamental and applied research.

Microscopes provide multidimensional images:

* 2D images (x, y),

* 3D images (diverse spectral channels or z),

* 4-5D combining spectral and/or temporal information,

* histological pyramidal images of tissues,

* high content screening images

* fluorescence lifetime images

Particular attention is paid to the formats of the saved data, with preference given to formats that allow the enrichment of metadata and formats that can be used by open-source software. Similarly, formats that allow the data to be saved in raw form, or possibly with lossless compression, are used.

Formats list: *.tif, *.lif, *.vsi, *.ome.tif, *.nd

All these formats are openable through BioFormat software, enable us to read, collect and use metadata of all images.

Type Image

Workpackage

Keywords (free-text) photonic microscopy, light microscopy, images

Language eng

Issued Date

Persistent identifier After publication, the images are deposited in a public archive and identified by DOI.

Identifier type DOI

May contain personal data? No

May contain sensible data? No

May take ethical issues into account? Yes

Will existing data be reused?
**Justification**

Images from photonic microscopes can be reused in a number of contexts:

1. analysis

2. complementary analyses

3. reuse by third-party researchers, provided that the image metadata are sufficiently enhanced

**How new data will be collected or produced?**

**Name of the method**

Photonic microscopy

**Description**

The images are obtained using proprietary acquisition software. Different file formats are generated depending on the acquisition software used. The data collected is saved locally, on the acquisition computer, on a data hard disk physically separate from the system hard disk, in a folder named after the team leader (Institut Cochin), or in a folder named after the unit external to the Institut Cochin, associated with the name of the team leader.

**Data Nature**

Experimental Data

**Equipments, technical platforms used**

• IMAG'IC : https://cat.opidor.fr/index.php/IMAG'IC

**Biological Samples**

**Research output description**

**Name**

Biological Samples

**Description**

The biological samples are of many kinds:

• Tissue slices

• Tissue cleared

• Prepared slides for SMLM and STED

• ExM (Expansion microscopy samples)

**Type**

Physical object

**Workpackage**

**Language**

eng

**Issued Date**

**Persistent identifier**

Researcher's one

**Identifier type**

Identifiant local

**May contain personal data?**

No

**May contain sensible data?**

No

**May take ethical issues into account?**

Yes
## Will existing data be reused?

### Justification

Biological samples can be re-used as often as necessary.

## How new data will be collected or produced?

### Name of the method
### Description

Vibratom, Clearing, SMLM slide preparation, Cell Biology

* **Tissue slices**

The tissues are recovered according to the protocols adapted to their origins, and are then cut using a vibratome located in the BSL2. The samples are tracked using the OpenIris website, allowing the prepared samples to be traced (their origins, the number of samples, the thickness of the cut).

* **Tissue cleared**

The fixed tissues (whole organs, slices or organoids) are recovered by the core facility after a request for service via the Open Iris website. The clarification protocol is defined with the user, and the sample is prepared in compliance with the procedures and protective measures appropriate to the chosen protocol.

* **Prepared slides for SMLM and STED**

Following a discussion between the user and the super-resolution microscopy experts, the appropriate protocol for the project (fixed or unfixed cells) is defined beforehand. Users then bring their samples to the core facility to finalise the sample mounting using the appropriate mounting buffer supplied by the expert.

* **ExM**

Following a discussion between the user and the core facility experts, the appropriate protocol for the project (choice of the expansion microscopy protocol) is defined. Then, user bring the stained samples (fixed tissue or fixed cells) to the core facility, and all the next steps are realised by the expert from gel preparation to imaging acquisition.

### Data Nature

Experimental data

### Equipments, technical platforms used

* IMAG'IC: https://cat.opidor.fr/index.php/IMAG'IC

## Image processing softwares

### Research output description
<table><tr><td>Name</td><td>Image processing softwares</td></tr><tr><td>Description</td><td>Via the CID database, the IMAG'IC core-facility provides a wide range of automated online image processing (Huygens deconvolution, CellPose segmentation, QuPath, ImageJ macros). On request, the core-facility also produces source code enabling users to carry out specific image processing. These programs can take the form of ImageJ macros or plugins, workflows with BitPlane IMARIS, CellPose, Ilastik software, or a combination of different software packages, known as workflows. The user will be trained in the use of these programmes.</td></tr><tr><td>Type</td><td>Software</td></tr><tr><td>Workpackage</td><td></td></tr><tr><td>Language</td><td>eng</td></tr><tr><td>Issued Date</td><td></td></tr><tr><td>May contain personal data?</td><td>No</td></tr><tr><td>May contain sensible data?</td><td>No</td></tr><tr><td>May take ethical issues into account?</td><td>Yes</td></tr></table>

## Will existing data be reused?

<table><tr><td>Justification</td><td>Image processing programmes developed for the users are intended to be reused for any useful purpose.</td></tr></table>

## How new data will be collected or produced?

<table><tr><td>Name of the method</td><td>Image Processing</td></tr><tr><td>Description</td><td>Source code is written according to user requirements. The code is commented on and users are trained in its use. Test processing is carried out using images supplied by the users, then ideally on model images with known expected results (ground truth).</td></tr><tr><td>Data Nature</td><td>Simulation data</td></tr><tr><td>Equipments, technical platforms used</td><td><ul><li>IMAG'IC : https://cat.opidor.fr/index.php/IMAG'IC</li></ul></td></tr><tr><td>Related references</td><td><ul><li>Macro ImageJ : https://imagej.net/ij/developer/index.html</li><li>CellPose : https://github.com/MouseLand/cellpose</li><li>QuPath : https://qupath.github.io/</li></ul></td></tr></table>

## Documentation and data quality
Light microscopy images

What metadata and documentation (for example way of organising data) will accompany the data?

<table><tr><td>Description</td><td>For quality, interpretation, reproducibility and sharing value, science data should be accompanied by detailed descriptions of the conditions that were used to produce them. For light microscopy, Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications.<br/>For the IMAG'IC core facility, when images are imported to the CID database, the machine metadata are automatically recorded as tags for archiving: [Microscope name, Acquisition software, Objectives, Lasers, Filtres, Tube, Acquisition date, User name].<br/>Users can also add sample tags: [Cell type, Tissue type, Staining, Protein, molecule, ...].<br/>It is thus possible to retrieve any data imported into the CID by searching for these machine or sample tags.</td></tr><tr><td>Metadata/data standards</td><td><ul><li>NBO-Q (4DN-BINA-OME-QUAREP Microscopy Metadata Specifications) : https://rdamsc.bath.ac.uk/api2/m111</li></ul></td></tr><tr><td>Metadata language code</td><td>eng</td></tr><tr><td>Documentation software</td><td>Bio-Formats</td></tr></table>

What methods will be used to ensure their scientific quality?
**Description**

The data generated on the IMAG'IC core facility comes from microscopes that are checked three times a year on seven measurement points (quality control procedure, as described in Faklaris et al., JCB (2022)) in order to optimize the reproducibility and therefore the quality of the data generated. The IMAG'IC core facility is a partner in the international consortium QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy) which works to improve quality control in photonic microscopy. A working group is working on the implementation of an image quality score.

The quality metadata are automatically calculated when each data is imported:

e.g. SNR SVI: calculation of the signal-to-noise ratio on 12bit for each image produced on IMAG'IC. There is one value per channel. This SNR SVI is used by the Huygens software to adapt the 3D deconvolution restoration to each type of signal.

WG10 of QUAREP-LiMi consortium also work on these topic trying to improve the image quality definition.

The IMAG'IC core facility is a partner of the ANR QUALIHEALTH which seeks to improve the quality of data in clinical and preclinical research. Data curation and formatting work is envisaged within this framework on the CID.

**Related references**

* Quality assessment in light microscopy for routine use through simple tools and robust metrics : 10.1083/jcb.202107093

**Biological Samples**

**What metadata and documentation (for example way of organising data) will accompany the data?**

**Description**

All data documentation are structured on electronical lab notebook CLEclassified by project.

We also use OpenIris website to collect requests for services.All these requests and services are archived.

**What methods will be used to ensure their scientific quality?**

**Description**

* Tissue slices

Visual inspection of the original tissue.

Visual inspection after vibratom slice and photonic microscopy quality.

* Tissue cleared

Visual inspection before and after the clearing

* Prepared slides for SMLM and STED

Photonic microscopy data quality.

* ExM

Photonic microscopy data quality.
## Image processing softwares

**What metadata and documentation (for example way of organising data) will accompany the data?**

**Description** For quality, interpretation, reproducibility and sharing value, science data should be accompanied by detailed descriptions of the conditions that were used to produce them. For image processing, IMAG'IC core-facility personnel comment code as much as possible.

**Metadata language code** eng

**Documentation software** Bio-Formats

**What methods will be used to ensure their scientific quality?**

**Description** Test processing is carried out using images supplied by the users, then ideally on model images with known expected results (ground truth).

## Legal and ethical requirements, codes of conduct

### Light microscopy images

**How will other legal issues, such as intellectual property rights and ownership, be managed?**

**What legislation is applicable?**

**Description** Promulgated in 2016, the Law for a Digital Republic (LRN) includes several measures on which the national open science policy is based. These measures are transposed, in particular, into the Research Code and the Code governing relations between the public and the administration (CRPA). IMAG'IC core facility follows these recommendations.

**Related references**

* Guide d'application de la Loi pour une République numérique pour les données de la recherche : 10.52949/31

**What ethical issues and codes of conduct are there, and how will they be taken into account?**
**Description**

The vast majority of samples imaged on our platform are fixed.

IMAG'IC provides microscopes at 3 different containment levels: BDSL1, 2 and 3, enabling users to handle living biological material at different levels of contamination risk.

Intravital imaging is performed under the ethical conditions laid down by law.
User are responsible about their APAFIS certification.

Any establishment that uses animals for scientific purposes must hold an accreditation. This is issued by a prefectural decree, following inspections by veterinary inspectors from the Departmental Directorate for Social Cohesion and Population Protection (DDPP or DDCSPP). To begin, any research project involving animals must obtain authorization from the Ministry of Research.
The authorization is granted for a maximum duration of 5 years, provided that the project has received a favorable evaluation from the ethics committee of the establishment where it will be carried out.

The core facility manager must ensure that the applicant complies with the legislation (Decree No. 2013-118 of February 1, 2013, concerning the protection of animals used for scientific purposes). The core facility manager can assist in drafting the project authorization request (APAFiS Platform on the website of the French Ministry of Higher Education and Research).

**Related references**

* JORF n°0032 du 7 février 2013 :
https://www.legifrance.gouv.fr/loda/id/JORFTEXT000027038013

**Biological Samples**

**How will other legal issues, such as intellectual property rights and ownership, be managed?**

**What legislation is applicable?**

**Description**

The data belong to the core facility users until their publication, at which point they become public.

**What ethical issues and codes of conduct are there, and how will they be taken into account?**

**Description**

Any establishment that uses animals for scientific purposes must hold an accreditation. This is issued by a prefectural decree, following inspections by veterinary inspectors from the Departmental Directorate for Social Cohesion and Population Protection (DDPP or DDCSPP). To begin, any research project involving animals must obtain authorization from the Ministry of Research.
The authorization is granted for a maximum duration of 5 years, provided that the project has received a favorable evaluation from the ethics committee of the establishment where it will be carried out.

The core facility manager must ensure that the applicant complies with the legislation (Decree No. 2013-118 of February 1, 2013, concerning the protection of animals used for scientific purposes). The core facility manager can assist in drafting the project authorization request (APAFiS Platform on the website of the French Ministry of Higher Education and Research).

**Related references**

* JORF n°0032 du 7 février 2013 :
https://www.legifrance.gouv.fr/loda/id/JORFTEXT000027038013
## Image processing softwares

**How will other legal issues, such as intellectual property rights and ownership, be managed?**

**What legislation is applicable?**

**Description**

The source code developed is the property of the coder and is made available
to the community on the platform's GitHub, under a CC BY NA licence.

**What ethical issues and codes of conduct are there, and how will they be taken into account?**

**Description**

CC BY NA

**Related references**

* Creative Commons rules : https://creativecommons.org/licenses/by-nc-sa/4.0/deed.fr

## Data processing and analysis

### Light microscopy images

**How and with what resources will the data be processed / analyzed?**
**Description**

To ensure the FAIR principle, an image processing workflow is copied to allow the exact same processing to be reproduced despite the constant evolution of software and its updates.

**Online processing**

Some processing can be done directly by the CID database, such as image restoration by 3D deconvolution. A "Huygens" script can be launched, via the CID, on one or all of the images in a dataset, directly at the import if necessary. Thus, the CID moves the raw images selected by the user to the computer or virtual machine containing the Huygens SVI software. Then the script launches the Huygens software with the semi-automatic parameters selected by the user and taken from the image's metadata. Once the processing is complete, the CID deletes the moved raw data and retrieves the resulting images and places them in a sub-dataset with the name Huygens. For each resulting image has been added in the processing metadata: itm, quality, scaleX, scaleZ, NA, binning, snrw, snrc, Ril

Other processing available online are dedicated to denoising, debluring, upsampling and segmentation using CellPose3. Whether for conventional-sized fluorescence images or for large pyramidal coded images, the CID can process these cases with CellPose either directly or in a QuPath environment.

**Quantitative analysis**

All the methods described before are also available on personal request.
IMAG'IC core facility also provides software resources as research output.

**Related references**

* Cellpose3: one-click image restoration for improved cellular segmentation : 10.1101/2024.02.10.579780

* Huygens Deconvolution: Restore microscopy images : https://svi.nl/Huygens-Deconvolution

* QuPath : https://qupath.github.io/

* Cellpose: a generalist algorithm for cellular segmentation : 10.1038/s41592-020-01018-x

**Equipments, technical platforms**

* IMAG'IC : https://cat.opidor.fr/index.php/IMAG'IC

**Biological Samples**

How and with what resources will the data be processed / analyzed?

**Description**

none

**Equipments, technical platforms**

* IMAG'IC : https://cat.opidor.fr/index.php/IMAG'IC

**Image processing softwares**

How and with what resources will the data be processed / analyzed?
**Description** The attached publication describes the issues involved in image processing. The softwares used by the core-facility has been described above.

**Related references**
* The crucial role of bioimage analysts in scientific research and publication : https://doi.org/10.1242/jcs.262322

**Equipments, technical platforms**
* IMAG'IC : https://cat.opidor.fr/index.php/IMAG'IC

## Storage and backup during the research process

### Light microscopy images

### How will data be stored and backed up during the research?
## Storage needs

For obvious security reasons, the connection of USB sticks or external hard disks is forbidden on the data acquisition machines.

As soon as the data is imported into the CID, it is archived and can be searched using the different tags accumulated during the import and the different processing and analysis. In all cases the raw data is kept intact, just as the results of processing or analysis will be new data linked to the raw data.

* Data that have been used to publish research must be accessible at any time.

* It is very important to keep the data that is usable at the state of the art of current research. The lack of short-term storage means that we must consider the notion of data quality and therefore retain only those data that have reliable and rich metadata, and those that allow us to answer a properly posed scientific question.

* It is therefore urgent to find a solution for storing data that has not been consulted for more than two years, for example, on a medium that does not clog up the storage of useful data in common use (storage on magnetic tapes, optical disks, etc.).

One of the main purposes of the CID DB is to allow the long-term archiving of this type of data. If the WEB server is attacked, it can be rebuilt at any time by the Image server. All the data are stored on an Image server in the premises of the Institut Cochin. A complete backup is made every day in one of the 4 other buildings of the Institut Cochin. If the Image server is damaged, a restoration is launched via this copy.

To summarize, the IMAG'IC IT architecture runs on 3 servers:

* Data server (backed up every day to a storage bay in another building)

* DMZ: for the imaging website (backed up every day on a storage bay in another building)

* MZ: Database server (no backup) a solution will have to be found here
All images are saved to the Cochin Image Database.

cf. INSTITUT COCHIN ENTITY DMP - CID

Storage requirements are indicated for an average year of data generation.

**Estimated volume of data**

10

**Unit**

TB

**Equipments, technical platforms**

* CID: https://cat.opidor.fr/index.php/CID

**Measures taken for data security**

CID access by institutional login and personal password.

## Biological Samples

**How will data be stored and backed up during the research?**

**Storage needs**

No storage, every samples are given to users.

**Measures taken for data security**

## Image processing softwares
## How will data be stored and backed up during the research?

**Storage needs**

Typically, the source code is stored on the programmer's computer. It is then made available to the user, either directly by network copy or on the CID. The size of the source files is negligible.

**Equipments, technical platforms**

* CID: https://cat.opidor.fr/index.php/CID

**Measures taken for data security**

CID access by institutional login and personal password.

# Data sharing and long-term preservation

## Light microscopy images

### How will data be shared?

**Modalities of sharing**

Raw data from research is increasingly in demand by publishers. Reproducibility in science is of utmost importance and providing raw data is one way to make the results of an experiment more reliable. Institut Cochin's researchers are therefore invited to deposit their raw data from a publication work on the CID (openData of Cochin Image Database). A direct download web page will then be generated and this link can be protected by a unique DOI (Digital Object Identifier). The IMAG'IC and GENOM'IC core facilities are responsible for generating this link. A contract has been signed with the OPIDOR service of the Inist-CNRS via the DataCite consortium: https://opidor.fr/identifier/

Also, once the images has been used for scientific publication, they are shared through public archive website BioImage Archive. The link is then identified with a DOI link that we are able to create.

**Reusability**

YES, with no condition

**Data repository/catalogs**

* BioImage Archive: https://cat.opidor.fr/index.php/BioImage Archive ()
* CID: https://cat.opidor.fr/index.php/CID ()

### How will data be long-term preserved? Which data?
**Justification** Every image is available on CID database for an amount of time which has not been defined yet.

**Estimated volume of data** 10

**Unit** TB

**Start date** 2024-01-01

**End date** 2024-12-31

**Final dispositions**

## Biological Samples

**How will data be shared?**

**Modalities of sharing** none

**Reusability**

**How will data be long-term preserved? Which data?**

**Justification** none

**Start date**

**End date**

**Final dispositions**

## Image processing softwares

**How will data be shared?**

**Modalities of sharing** For the purposes of scientific reproducibility, the source codes are made available to the community after publication of the data on the IMAG'IC platform's GitHub.
[https://github.com/IMAG-IC/](https://github.com/IMAG-IC/)

**Reusability** YES, under CC BY SA licence.

**Data repository/catalogs**
* CID : [https://cat.opidor.fr/index.php/CID ()](https://cat.opidor.fr/index.php/CID ())

**How will data be long-term preserved? Which data?**
**Justification**

Ideally, proven source code can be stored on the dedicated Software Heritage site.

**Start date**

**End date**

**Archive**

**Title** Software Heritage

**Repository ID** https://cat.opidor.fr/index.php/Software_Heritage

**Identifier type** URL

**Geo location (country)** FR

**Certification**

**PID system** SWHID

**Available metadata standards**

**Final dispositions**