Update README.md

README.md

@@ -1,52 +1,52 @@
 ---
 dataset_info:
   features:
-  - name: image
-    dtype: image
-  - name: label
-    dtype:
-      class_label:
-        names:
-          0: control
-          1: sick
+    - name: image
+      dtype: image
+    - name: label
+      dtype:
+        class_label:
+          names:
+            0: control
+            1: sick
   config_name: SDH_16k
   splits:
-  - name: test
-    num_bytes: 683067
-    num_examples: 3358
-  - name: train
-    num_bytes: 2466024
-    num_examples: 12085
-  - name: validation
-    num_bytes: 281243
-    num_examples: 1344
+    - name: test
+      num_bytes: 683067
+      num_examples: 3358
+    - name: train
+      num_bytes: 2466024
+      num_examples: 12085
+    - name: validation
+      num_bytes: 281243
+      num_examples: 1344
   download_size: 2257836789
   dataset_size: 3430334
 annotations_creators:
-- expert-generated
+  - expert-generated
 language: []
 language_creators:
-- expert-generated
+  - expert-generated
 license:
-- agpl-3.0
+  - agpl-3.0
 multilinguality: []
 pretty_name: SDH staining muscle fiber histology images used to train MyoQuant model.
 size_categories:
-- 10K<n<100K
+  - 10K<n<100K
 source_datasets:
-- original
+  - original
 tags:
-- myology
-- biology
-- histology
-- muscle
-- cells
-- fibers
-- myopathy
-- SDH
-- myoquant
+  - myology
+  - biology
+  - histology
+  - muscle
+  - cells
+  - fibers
+  - myopathy
+  - SDH
+  - myoquant
 task_categories:
-- image-classification
+  - image-classification
 ---
 
 # Dataset Card for MyoQuant SDH Data
@@ -56,119 +56,107 @@ task_categories:
 - [Table of Contents](#table-of-contents)
 - [Dataset Description](#dataset-description)
   - [Dataset Summary](#dataset-summary)
-  - [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
-  - [Languages](#languages)
 - [Dataset Structure](#dataset-structure)
-  - [Data Instances](#data-instances)
-  - [Data Fields](#data-fields)
-  - [Data Splits](#data-splits)
-- [Dataset Creation](#dataset-creation)
-  - [Curation Rationale](#curation-rationale)
-  - [Source Data](#source-data)
-  - [Annotations](#annotations)
+  - [Data Instances and Splits](#data-instances-and-splits)
+- [Dataset Creation and Annotations](#dataset-creation-and-annotations)
+  - [Source Data and annotation process](#source-data-and-annotation-process)
+  - [Who are the annotators ?](#who-are-the-annotators)
   - [Personal and Sensitive Information](#personal-and-sensitive-information)
 - [Considerations for Using the Data](#considerations-for-using-the-data)
   - [Social Impact of Dataset](#social-impact-of-dataset)
-  - [Discussion of Biases](#discussion-of-biases)
-  - [Other Known Limitations](#other-known-limitations)
+  - [Discussion of Biases and Limitations](#discussion-of-biases-and-limitations)
 - [Additional Information](#additional-information)
-  - [Dataset Curators](#dataset-curators)
   - [Licensing Information](#licensing-information)
   - [Citation Information](#citation-information)
-  - [Contributions](#contributions)
+- [The Team Behind this Dataset](#the-team-behind-this-dataset)
+- [Partners](#partners)
 
 ## Dataset Description
 
-- **Homepage:**
-- **Repository:**
-- **Paper:**
-- **Leaderboard:**
-- **Point of Contact:**
+- **Homepage:** https://github.com/lambda-science/MyoQuant
+- **Repository:** https://huggingface.co/corentinm7/MyoQuant-SDH-Model
+- **Paper:** Yet To Come
+- **Leaderboard:** N/A
+- **Point of Contact:** [**Corentin Meyer**, 3rd year PhD Student in the CSTB Team, ICube — CNRS — Unistra](https://cmeyer.fr) email: <corentin.meyer@etu.unistra.fr>
 
 ### Dataset Summary
 
-[More Information Needed]
-
-### Supported Tasks and Leaderboards
-
-[More Information Needed]
-
-### Languages
-
-[More Information Needed]
+This dataset contains images of individual muscle fiber used to train [MyoQuant](https://github.com/lambda-science/MyoQuant) SDH Model. The goal of these data is to train a tool to classify SDH stained muscle fibers depending on the presence of mitochondria repartition anomalies. A pathological feature useful for diagnosis and classification in patient with congenital myopathies.
 
 ## Dataset Structure
 
-### Data Instances
-
-[More Information Needed]
-
-### Data Fields
+### Data Instances and Splits
 
-[More Information Needed]
+A total of 16 787 single muscle fiber images are in the dataset, split in three sets: train, validation and test set.  
+See the table for the exact count of images in each category:  
+| | Train (72%) | Validation (8%) | Test (20%) | TOTAL |
+|---------|-------------|-----------------|------------|-------------|
+| control | 9165 | 1019 | 2546 | 12730 (76%) |
+| sick | 2920 | 325 | 812 | 4057 (24%) |
+| TOTAL | 12085 | 1344 | 3358 | 16787 |
 
-### Data Splits
+## Dataset Creation and Annotations
 
-[More Information Needed]
+### Source Data and annotation process
 
-## Dataset Creation
+To create this dataset of single muscle images, whole slide image of mice muscle fiber with SDH staining were taken from WT mice (1), BIN1 KO mice (10) and mutated DNM mice (7). Cells contained within these slides manually counted, labeled and classified in two categories: control (no anomaly) or sick (mitochondria anomaly) by two experts/annotators. Then all single muscle images were extracted from the image using CellPose to detect each individual cell’s boundaries. Resulting in 16787 images from 18 whole image slides.
 
-### Curation Rationale
+### Who are the annotators?
 
-[More Information Needed]
+All data in this dataset were generated and manually annotated by two experts:
 
-### Source Data
+- [**Quentin GIRAUD, PhD Student**](https://twitter.com/GiraudGiraud20) @ [Department Translational Medicine, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/recherche/teams/pathophysiology-of-neuromuscular-diseases), 1 rue Laurent Fries, 67404 Illkirch, France <quentin.giraud@igbmc.fr>
+- **Charlotte GINESTE, Post-Doc** @ [Department Translational Medicine, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/recherche/teams/pathophysiology-of-neuromuscular-diseases), 1 rue Laurent Fries, 67404 Illkirch, France <charlotte.gineste@igbmc.fr>
 
-#### Initial Data Collection and Normalization
+A second pass of verification was done by:
 
-[More Information Needed]
+- **Bertrand VERNAY, Platform Leader** @ [Light Microscopy Facility, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/plateformes-technologiques/photonic-microscopy), 1 rue Laurent Fries, 67404 Illkirch, France <bertrand.vernay@igbmc.fr>
 
-#### Who are the source language producers?
-
-[More Information Needed]
-
-### Annotations
-
-#### Annotation process
+### Personal and Sensitive Information
 
-[More Information Needed]
+All image data comes from mice, there is no personal nor sensitive information in this dataset.
 
-#### Who are the annotators?
+## Considerations for Using the Data
 
-[More Information Needed]
+### Social Impact of Dataset
 
-### Personal and Sensitive Information
+The aim of this dataset is to improve congenital myopathies diagnosis by providing tools to automatically quantify specific pathogenic features in muscle fiber histology images.
 
-[More Information Needed]
+### Discussion of Biases and Limitations
 
-## Considerations for Using the Data
+This dataset has several limitations (non-exhaustive list):
 
-### Social Impact of Dataset
+- The images are from mice and thus might not be ideal to represent actual mechanism in human muscle
+- The image comes only from two mice models with mutations in two genes (BIN1, DNM) while congenital myopathies can be caused by a mutation in more than 35+ genes.
+- Only mitochondria anomaly was considered to classify cells as "sick", other anomalies were not considered, thus control cells might present other anomalies (such as what is called "cores" in congenital myopathies for examples)
 
-[More Information Needed]
+## Additional Information
 
-### Discussion of Biases
+### Licensing Information
 
-[More Information Needed]
+This dataset is under the GNU AFFERO GENERAL PUBLIC LICENSE Version 3, to ensure that what's open-source, stays open-source and available to the community.
 
-### Other Known Limitations
+### Citation Information
 
-[More Information Needed]
+MyoQuant publication with model and data is yet to come.
 
-## Additional Information
+## The Team Behind this Dataset
 
-### Dataset Curators
+**The creator, uploader and main maintainer of this dataset, associated model and MyoQuant is: [Corentin Meyer, 3rd year PhD Student in the CSTB Team, ICube — CNRS — Unistra](https://cmeyer.fr) Email: <corentin.meyer@etu.unistra.fr> Github: [@lambda-science](https://github.com/lambda-science)**
 
-[More Information Needed]
+Special thanks to the experts that created the data for this dataset and all the time they spend counting cells :
 
-### Licensing Information
+- **Quentin GIRAUD, PhD Student** @ [Department Translational Medicine, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/recherche/teams/pathophysiology-of-neuromuscular-diseases), 1 rue Laurent Fries, 67404 Illkirch, France <quentin.giraud@igbmc.fr>
+- **Charlotte GINESTE, Post-Doc** @ [Department Translational Medicine, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/recherche/teams/pathophysiology-of-neuromuscular-diseases), 1 rue Laurent Fries, 67404 Illkirch, France <charlotte.gineste@igbmc.fr>
 
-[More Information Needed]
+Last but not least thanks to Bertrand Vernay being at the origin of this project:
 
-### Citation Information
+- **Bertrand VERNAY, Platform Leader** @ [Light Microscopy Facility, IGBMC, CNRS UMR 7104](https://www.igbmc.fr/en/plateformes-technologiques/photonic-microscopy), 1 rue Laurent Fries, 67404 Illkirch, France <bertrand.vernay@igbmc.fr>
 
-[More Information Needed]
+## Partners
 
-### Contributions
+<p align="center">
+  <img src="https://i.imgur.com/m5OGthE.png" alt="Partner Banner" style="border-radius: 25px;" />
+</p>
 
-Thanks to [@github-username](https://github.com/<github-username>) for adding this dataset.
+MyoQuant-SDH-Data is born within the collaboration between the [CSTB Team @ ICube](https://cstb.icube.unistra.fr/en/index.php/Home) led by Julie D. Thompson, the [Morphological Unit of the Institute of Myology of Paris](https://www.institut-myologie.org/en/recherche-2/neuromuscular-investigation-center/morphological-unit/) led by Teresinha Evangelista, the [imagery platform MyoImage of Center of Research in Myology](https://recherche-myologie.fr/technologies/myoimage/) led by Bruno Cadot, [the photonic microscopy platform of the IGMBC](https://www.igbmc.fr/en/plateformes-technologiques/photonic-microscopy) led by Bertrand Vernay and the [Pathophysiology of neuromuscular diseases team @ IGBMC](https://www.igbmc.fr/en/igbmc/a-propos-de-ligbmc/directory/jocelyn-laporte) led by Jocelyn Laporte