Merge pull request #423 from gletort/cellposeappose-doc

Cellposeappose doc

Author: tinevez

_pages/plugins/cellpose-appose.md

@@ -0,0 +1,50 @@
+---
+title: Cellpose-Appose 
+description: PLugin to use Cellpose from Fiji relying on Appose.
+artifact: fiji.plugin:Cellpose_Appose
+categories: [Segmentation]
+---
+
+
+This is a plugin to install and run [cellpose](https://www.cellpose.org/) on 2D/3D in Fiji. 
+Two version of cellpose is available:
+- Cellpose (v3)
+- Cellpose-SAM (v4)
+
+This plugin is based on [Appose](https://github.com/apposed/appose), that automatically install python environment and allows python script execution with shared objects with Fiji.
+
+## Installation
+
+You can install the plugin for the unliste update site `Appose-Playground`:
+in Fiji, go to `Help>Update...` then to `Manage Update Sites` in the window that opens.
+Click `Add unliste update site`, name it `Appose-Playground` and write its address `https://sites.imagej.net/Appose-Playground`.
+
+Select the Appose-Cellpose `.jar` file to install only this plugin, or keep all proposed plugins. 
+Press `Apply changes` and restart Fiji when it's done.
+
+> [!IMPORTANT]
+> You should have a recent version of Fiji, based on Java 21 or more. Download a new version if you're current installation is too old.
+
+## Usage
+
+From Fiji
+- Open the image that you want to process.  
+- Launch one of the cellpose version available in the plugin:
+  - `Plugins>Segmentation>Cellpose-Appose>Cellpose...` _see [here](#cellpose) for documentation_
+  - `Plugins>Segmentation>Cellpose-Appose>Cellpose-SAM...` _see [here](#cellpose-sam) for documentation_
+- Configure your Cellpose run through the Graphic Interface
+- Press "Ok" and Enjoy!   
+
+> [!NOTE]
+> The python environment will be automatically installed in your home `.local\shared\appose` directory and activated from the plugin when needed.
+
+
+## Cellpose
+
+The option `Plugins>Segmentation>Cellpose-Appose>Cellpose...` allows to run CellPose v3.
+
+## Cellpose-SAM
+
+The option `Plugins>Segmentation>Cellpose-Appose>Cellpose-SAM...` allows to run CellPose v4 with SAM.
+
+### Cuda selection