diff --git a/README.md b/README.md index f33803b..8485b45 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,12 @@ # Biological Image Analysis Project: Case study of leaf epithelium -Projet "guidé" pour mettre en pratique ces connaissances en analyse d'image. -Vous serez évalué sur votre capacité à construire une base de données, créé une mini-package python pour répondre à trois objectifs et à les documenter. +A guided project to put your knowledge of image analysis into practice. You will be assessed on your ability to build a database, create a python mini-package to resolve three goals and document them. ## Dataset and Motivation -The proposed dataset for this project is accessible on Zenedo https://zenodo.org/record/5001583. +The proposed dataset for this project is accessible on [Zenedo](https://zenodo.org/record/5001583). You should download the `cellImages.zip` file and unzip it in the `data` folder. -Note that this dataset is very diverse. You will have to choose a subset of the data to work on and document your choice in the data `README.md` file. +Note that this dataset is very diverse. You will have to choose a subset of the data to work on and document your choice in the data `README.md` file. In `data` you can find some examples of this dataset. ## Motivation @@ -50,6 +49,7 @@ Take time to understand the following notions and find your own definitions: There are three main goals for this project. Take a moment with a pen and paper to write down your pipeline ideas and connect them between each other. This is a good way to find a first structure draft for your code. All the use cases should be implemented in the same python package in the `src` folder. + ### Dataset: Leaf Epithelium This dataset is composed of pair of "leaf-level" images and "cell-level" images. You have to use the cell-level images to answer the following questions. You can use the leaf-level images to help you understand the dataset if you are curious about the plant. @@ -85,8 +85,8 @@ Here we will look at specific cell organisation: can we find junction shared by This could be the first step to get the dynamic of the epithelium, if the dataset includes time-lapse images, you could try to track the junctions over time. But this is not the goal of this project (yet!). -![cell intercalation](https://royalsocietypublishing.org/cms/asset/37d124f8-7640-4a56-82de-15aa0391f819/rstb20170328f02.jpg) - +![image](https://user-images.githubusercontent.com/94049435/228680990-9797f8fc-a57c-4762-9285-1d478c43d781.png) +from Tetley Robert J. and Mao Yanlan 2018 The same but different: cell intercalation as a driver of tissue deformation and fluidity Phil. Trans. R. Soc. B3732017032820170328 http://doi.org/10.1098/rstb.2017.0328 > **Note** > - You want to check if there are junction where more than 3 cells are touching each other. @@ -105,6 +105,7 @@ You can find an example in the folder `results/how_are_cells_connected`. Please > - Discuss the results and the limits in the README.md ![fig 6 of sapala](https://iiif.elifesciences.org/lax/32794%2Felife-32794-fig6-v2.tif/full/,1500/0/default.jpg) +from A. Sapala et al., “Why plants make puzzle cells, and how their shape emerges,” eLife, vol. 7, p. e32794, Feb. 2018, doi: 10.7554/eLife. ## Deliverable @@ -207,4 +208,7 @@ The different *presentations*: (*How to share, Architecure and feedback*) are no ## Contributing -You can contribute to this project by forking the repository and submitting a pull request. We will review your changes and merge them into the main repository if they are relevant. \ No newline at end of file +You can contribute to this project by forking the repository and submitting a pull request. We will review your changes and merge them into the main repository if they are relevant. + +Contributors: Clément Caporal, Camille Duquesne and Louise Dagher +This projected has been created for the [Learning Planet Institute bachelor](https://licence.learningplanetinstitute.org/en)