Mettre à jour README.md (d8c735b2) · Commits · Nicolas Elie / REDPOL-open

README.md

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Changes for README.md: 5 added lines, 1 removed line.
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		@@ -31,6 +31,9 @@ The proposed installation uses Conda environment: https://docs.conda.io/en/lates
		4. You can install an environment via the provided environment file(s): installationEnv.yml.
		> <span dir="">conda env create -f</span> installationEnv.yml


		# Procedure

		#### To test the execution of the AnalyzeSequence.ipynb program

		The AnalyzeSequence.ipnyb program allows to use our Stardist model on each image of the vsi file.
		@@ -51,10 +54,11 @@ Run _AnalyzeSequence.ipnyb_ program on conda environment
		> Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. _Scientific Reports_ (2017). \
		> https://doi.org/10.1038/s41598-017-17204-5

		INSERT UN EXEMPLE IMAGE QUAPTH AVEC CONTOURS et CLASSES

		On your images, annotate the objects that interest you. If you have categories, remember to declare the different classes. For details on how to use Qupath, see the documentation on their site.

		![QUPATH ILLUSTRATION](https://git.unicaen.fr/nicolas.elie/redpol-open/-/raw/master/media/qupath.jpg)

		2. Once your annotations are done, use the script "_Export Annotations gson.groovy_" to export the annotations as a json file in Qupath.
		3. Then use the python program "_JSON_Qupath_to_ImageLabel.ipynb_" which will allow to format the images and annotations so that they can be used by the program "_Model_Build.ipynb_." This program is directly from an example provided on the github Stardist repository.