Commit 7960fdc3 authored by Nicolas Elie's avatar Nicolas Elie
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Mettre à jour README.md

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+12 −4
Changes for README.md: 12 added lines, 4 removed lines.
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@@ -75,7 +75,10 @@ The AnalyzeSequence.ipnyb program allows to use our Stardist model on each image

The program process a detection and classification of chromatophores and save a file results.

In this project, a example file is given : 'Examples/Process_13.vsi' as well as our model Stardist Model :  'models/stardist_multiclass'
In this project, We provide an image and our model to test our programs : 

- 'Examples/Process_13.vsi' 
-  Our model Stardist Model :  'models/stardist_multiclass'

To test programs without use command lines :

@@ -104,19 +107,24 @@ On your images, annotate the objects that interest you. If you have categories,
![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.
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_." 
It is possible to test code with a small series with images examples :
-  _Examples/0001.tif_ and _Examples/0001b.tif_ 
-  JSON files on _Examples/qupathProject/ExportJSON_

```
jupyter nbconvert --execute --clear-output JSON_Qupath_to_ImageLabel.ipynb
```

4. Configure and execute _Model_Build.ipynb_
4. Configure and execute _Model_Build.ipynb_.

This program is directly from an example provided on the github Stardist repository.

```
jupyter nbconvert --execute --clear-output Model_Build.ipynb
```

It is possible to test code with a small series with images examples : _Examples/0001.tif_ and _Examples/0001b.tif_ and JSON files on _Examples/qupathProject/ExportJSON_
It is possible to test code with a small series with images examples : 0001.tif and 0001b.tif and JSON files

```
jupyter nbconvert --execute --clear-output Model_Build_short_example.ipynb