INSTITUT COCHIN ENTITY DMP - PIV Core
Facility

Gilles Renault, Thomas Guilbert

► To cite this version:

Gilles Renault, Thomas Guilbert. INSTITUT COCHIN ENTITY DMP - PIV Core Facility. Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Cité, F-75014 Paris, France. 2024, https://institutcochin.fr/plateformes/piv. hal-04834265v2

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Submitted on 18 Dec 2024

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# INSTITUT COCHIN ENTITY DMP - PIV

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 - PIV

**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** 2024-07-18

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

**Identifier** https://doi.org/10.57889/pivCF

**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 - PIV</td></tr><tr><td>Acronym</td><td>PIV</td></tr><tr><td>Identifier</td><td>https://institutcochin.fr/plateformes/piv</td></tr><tr><td>Identifier type</td><td>URL</td></tr><tr><td>Description</td><td>The core facility handles the various phases of your in vivo imaging projects: advice on experimental design, image acquisition and analysis, and delivery of results. It has the facilities to house animals for the duration of the study.<br>The platform is part of the Université Paris Cité's Plateforme Imageries du Vivant (PIV), which brings together all the pre-clinical imaging modalities at university level (μIRM, μCT, μTEP, iRPE, etc.) as well as a number of clinical imaging research modalities.</td></tr></table>

<table><tr><td>Creation date</td><td>2005-12-01</td></tr></table>

## Research outputs :

1. Measurements and associated calculations (Dataset)

2. Images (Image)

## Contributors
<table><thead><tr><td>Name</td><td>Affiliation</td><td>Roles</td></tr></thead><tbody><tr><td>Bibaki Giovanna</td><td>Institut Cochin - 051sk4035</td><td>• Data Collector (Measurements, Images, Measurements, Images)</td></tr><tr><td>Guilbert Thomas - 0000-0001-5069-0730</td><td>Institut Cochin - 051sk4035</td><td>• DMP manager</td></tr><tr><td>Lager Franck</td><td>Institut Cochin - 051sk4035</td><td>• Data Collector (Measurements, Images, Measurements, Images)</td></tr><tr><td>Lagoutte Isabelle</td><td>Institut Cochin - 051sk4035</td><td>• Data Collector (Measurements, Images, Measurements, Images)</td></tr><tr><td>Monbernard Pierre</td><td>Institut Cochin - 051sk4035</td><td>• Data Collector (Measurements, Images, Measurements, Images)</td></tr><tr><td>Renault Gilles - 0000-0003-2273-1229</td><td>Institut Cochin - 051sk4035</td><td>• Contact Person (Measurements, Images)<br>• DMP Manager (Measurements)<br>• Data Collector (Measurements)<br>• Entity's Manager (Measurements, Images, Measurements, Measurements, Measurements, Images, Images, Images, Measurements, Measurements, Images, Images, Measurements)<br>• Entity's manager</td></tr></tbody></table>
## Data description and collection or re-use of existing data

### Measurements and associated calculations

#### Research output description

**Name** Measurements and associated calculations

**Description**
* Measurements performed in Image acquisitions :
* Anatomical dimensions (length, surface, Volume)
* Velocities (peak velocities, mean velocities, gradients, time intervals)
* Associated functional or anatomical parameters (Volume, Ejection Fraction, Cardiac output)
* Deformation related informations (strain and strain rate)
* Doppler-related informations (Percentage of pixels showing flow from Power Doppler), Velocities
* Optoacoustic signal
* Contrast uptake values
* Bioluminescence signal parameters (photon flux)

**Type** Dataset

#### Workpackage

**Keywords (free-text)** in vivo imaging, ultrasound, bioluminescence, Doppler

**Language** eng

#### Issued Date

**May contain personal data?** No

**May contain sensible data?** No

**May take ethical issues into account?** Yes

#### Will existing data be reused?

**Justification** May be used by third-party researchers and complementary analyses

#### How new data will be collected or produced?
**Name of the method** In vivo Imaging

**Description** From acquired image datasets, various softwares allow to produce measures. These measurements are summarized in tablesheet.

**Data Nature** Experimental Data

**Equipments, technical platforms used**
* PIV : https://cat.opidor.fr/index.php/PIV

## Images

### Research output description

**Name** Images

**Description**
* Ultrasound images or image sequences (Bmode, Power and color Doppler images, Contrast ultrasound images, optoacoustic images, all in 2D or 3D)
* Time-motion images (TM mode)
* Pulsed Doppler flow (velocity x time)
* Bioluminescence images (2D photo, and overlay of photon flux)

**Type** Image

**Workpackage**

**Keywords**
* bioluminescence (Thésaurus INRAE)
* échographie (Thésaurus INRAE)

**Keywords (free-text)**

**Issued Date**

**May contain personal data?** No

**May contain sensible data?** No

**May take ethical issues into account?** Yes

**Will existing data be reused?**

**Justification** Images or image sequences are rarely used but can be. For further measurements or quantification.

**How new data will be collected or produced?**
**Name of the method** Ultrasound and bioluminescence Imaging

**Description**

**Ultrasound Imaging:**

Data will be acquired using various ultrasound Machines. In most research project, images are acquired on anesthetized animals, but acquisitions can be performed to explore some soft material properties. Briefly ultrasound imaging devices emit ultrasound and collect reflected echoes from soft tissues and eventually generate images or measure Doppler signals. An image is acquired on a single animal, imaging only parts of soft tissues of the animal.

* Visualsonics machine (VEVO F2 and VEVO 2100): These systems use high resolution imaging systems running high frequency probes (15 to 60MHz central frequency), leading to images with resolution up to 40µm. Images are acquired using the proprietary software running the system. The system produces anatomical B mode images, Power or Color Doppler images, Non linear contrast images, shear wave elastography images or optoacoustic images. These images can be a single image or 2D+t image sequences. Lastly these images can be acquired in 3D. Additionally, there are Pulsed Wave Doppler traces showing blood flow velocities or Time Motion mode showing 1D data over time. These images are acquired live to frame rates up to 200 images per second, stored in the machine and eventually exported for archiving or measurement using proprietary software (VEVO Lab, Visualsonics).

* Aixplorer (Supersonic Imagine): This system is a clinical device, tuning probes between 3 to 15MHz. Probes, leading to resolution up to 250µm. Images are acquired using the proprietary software running the system. The system produces anatomical B mode images, Power or Color Doppler images, Shear Wave Elastography images. These images can be a single image or 2D+t image sequences. Additionally, there are Pulsed Wave Doppler traces showing blood flow velocities. These images are acquired live to frame rates up to 70 images per second, stored in the machine and eventually exported for archiving. Measurement are being done using the proprietary software on the machine.

* Verasonics Vantage 256: This machine is a high frame rate programmable ultrasound system. It is run using proprietary libraries running using Matlab Software. It can acquire images up to 10000 images per second, and can run ultrasound probes up to 30MHz. The images are stored in a Matlab Format and are processed with user developed software in matlab to generate images. The Raw data or IQ data can be stored for further analysis.

**Bioluminescence imaging**

The data is collected with an Optima RT (BiospaceLabs, France) system. This system acquires photons coming out of up to 5 mice in a single data acquisition. The system collects photons on a CCD Camera after photoamplification allowing real time photon acquisition. The data is stored in a proprietary format based on list file format (similar to nulcea medicine file format, listing the coordinates of each single photon count by the machine). Data is presented as images integrating photon count over time. This photon count can be recalculated after acquisition, changing the integration window. The result image can be displayed in counts of photon, counts per minute, photons, photons per second, photons per second per steradian, photons per second per steradiants per cm².

this data, save in a proprietary file format is archived and can further analyzed using the M3 Vision proprietary software.

The machine produces three types of images: photographs of the animals being imaged, fluorescence images and bioluminescence images. Fluorescence images are generated after appropriate selection of excitation and emission filters with integration times about a few milliseconds. Bioluminescence images are acquired without excitation, collected photons emitted by bioluminescence of chemiluminescence reaction in vivo (luciferase-luciferin, luminol,...).
**Data Nature** Experimental data

**Equipments, technical platforms used**

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

## Documentation and data quality

### Measurements and associated calculations

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

**Description**
Original datasets generated by image analysis software are stored. Datasets allways include, name of the animal, date of acquisition. Each parameter is reported as column title together with the unit used.

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

**Description**
1- outlier detection on repeated measures
2- coherence of the number of expected measures compared to actual measures.

### Images

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

**Description**
* Name of the image
* Identification of the animal
* Acquisition date
* Acquisition parameters

**Metadata/data standards**
* REMBI (Recommended Metadata for Biological Images) : https://rdamsc.bath.ac.uk/api2/m112

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

There is no calibration controlled method for ultrasound images right now : not applicable.

Bioluminescence: Image of background signal, allowing to measure the noise level and check reference diode for luminescence.

## Legal and ethical requirements, codes of conduct

### Measurements and associated calculations

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

**What legislation is applicable?**

**Description**

Pre clinical images can only be acquired if the animal experimentation project as been recorded and approved by the french ministry of research.

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

**Description**

* animal experimentation is strongly regulated by european and french laws. Each project has been evaluated by local ethics comitee

### Images

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

**What legislation is applicable?**

**Description**

Pre clinical images can only be acquired if the animal experimentation project as been recorded and approved by the french ministry of research.

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

**Description**

Animal experimentation is strongly regulated by european and french laws. Each project has been evaluated by local ethics comitee.

## Data processing and analysis
## Measurements and associated calculations

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

**Description** Raw data are summarized in tablesheet files and further processed for statistical analyses.

**Equipments, technical platforms**
* PIV: https://cat.opidor.fr/index.php/PIV

## Images

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

**Description** Images will be processed by proprietary image analysis software provided by the acquisition device manufacturer.

These software allow the generation of measurements. The manufacturer's documentation explains how data has to be processed and how calculations are performed.

**Equipments, technical platforms**
* PIV: https://cat.opidor.fr/index.php/PIV

## Storage and backup during the research process

### Measurements and associated calculations

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

**Storage needs** Measurements and associated analyses are stored for 5 years on the facility's server.

Open CID is a solution that should be adopted soon.

**Estimated volume of data** 500

**Unit** MB

**Equipments, technical platforms**
* CID: https://cat.opidor.fr/index.php/CID

**Measures taken for data security**
## Images

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

**Storage needs**

Images and image sequences are stored for 5 years on the facility's server.
Open CID is a solution that should be adopted soon.

**Unit** GB

**Equipments, technical platforms**

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

**Measures taken for data security**

## Data sharing and long-term preservation

### Measurements and associated calculations

**How will data be shared?**

**Modalities of sharing**

Most of data are sent by emails or through institutional file sharing services.
CID is also an available solution.

**Reusability**

Yes, if contribution is acknowledged.

**Data repository/catalogs**

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

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

**Justification**

Measurements and associated analyses are stored for 5 years on the facility's server.
Open CID is the storage solution that will be implemented soon.

**Unit** MB

**Start date**

**End date**

**Final dispositions**

## Images
## How will data be shared?

**Modalities of sharing** Using CID or file sharing service.

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

**Data repository/catalogs**

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

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

**Justification**
Images are stored for 5 years on the facility's server.
Open CID is the storage solution that will be implemented soon.

**Unit** MB

**Start date**

**End date**

**Final dispositions**