Doc

docs/home.md

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+# Fish&Feats ![snap](imgs/snap.png)
+
+## Usage
+You can launch `fishfeats` in Napari by going to `Plugins>fishfeats>Start`. It will open a file dialog box asking you to select the image that you want to analyze. Possible input formats are currently `.tif, .czi, .ims`. You can open an issue to ask for another file format to be added.
+
+Then the image will be displayed, with the different channels shown as separated layers on the left panel.
+
+### Outputs/Setup
+All the outputs of `fishfeats` will be saved in the folder called `results` that will be automatically created in the folder containing your image. If you run `fishfeats` again on the same image, the program will look into that folder for already saved files, so that you can load previous files and don't have to redo all the steps from scratch.
+
+At each step, the parameters that you used for your current image are saved in the associated configuration file (in the `results` folder, the file `yourimagename.cfg`) and will be reloaded each time you redo the same step.
+
+From version 1.2 of FishFeats, for all steps, measures are saved in the same file in the `results` folder, called `yourimagename_results.csv`. You can open this file out of the pipeline with any software for tabular data reading/analysis (Excel, R..) and analyse/extract the desired columns. 
+
+
+### Main features
+
+`fishfeats` proposes several analyses steps in the main interface:
+
+- [Image scalings](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Image-scalings): set the global parameter of the image to analyse (scalings, channels)
+- [Get cells](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Get-cells): segment/load/correct the cell apical contours in 2D
+- [Load junctions from default file](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Load-junctions-from-default-file): directly load the file containing the segmented cells and create the corresponding cells.
+- [Get nuclei](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Get-nuclei): segment/load/correct the nuclei in 3D.
+- [Separate junctions and nuclei](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Separate-junctions-and-nuclei): if the junctions staining and nuclei staining are in the same channel, to segment them it is necessary to separate them before with this step.
+- [Get RNAs](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Get-rnas): segment/assign/correct/measure the RNAs in one or more RNA channel.
+- [Classify cells](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Classify-cells): manually classify the segmented cells with a user defined criteria (eg "PCNA or not"). Can be automatically prefilled then manually corrected.
+- [Measure cytoplasmic staining](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Measure-cytoplasmic-staining) to measure the intensity of one or more channels in each segmented cell around the surface.
+
+![main](uploads/637aa10aedd44698849fbbf13af9cddc/main.png)
+
+When you open a new image, the plugin will directly go to the first mandatory steps of fixing the image scales and channels (image scalings).
+
+### General shortcuts
+
+For each step, **FishFeats** proposes shortcuts to make its use more agreable/user-friendly, aditionnaly to the ones already proposed by Napari. The specific shortcuts are indicated in the text overlay showed at the top left side of the view. 
+You can always type <kbd>h</kbd> to show/hide these help messages.
+
+A few other shortcuts are always available:
+* **Napari default shortcuts**: go to `File>Preferences>Shortcuts` to see the list of available shortcuts, associated with each kind of layers
+* Press <kbd>h</kbd>: show/hide current help message
+* Press <kbd>Control-p</kbd> to activate/desactive vispy visualisation mode in 3D. This mode allows you to control the visualisation angle, but can inactive some selection tools.
+* Press <kbd>F1</kbd> to show/hide the first layer (from the list of layers in the left bottom part of the window, starting from the bottom). By default, the first layer should be your input image first color chanel, called `originalImageChanel0` in FishFeats.
+* Press <kbd>F2</kbd> to show/hide the second layer, <kbd>F3</kbd> for the third layer...
+
+
+
+### Hierarchical clustering
+
+You can launch this analysis with `Plugins>fishfeats>Hierarchical clustering`.
+It will perform hierarchical clustering on a set of columns (that contains RNA counts for example) and show the resulting clustering on the segmented cells. 
+See [Hierarchical clustering](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Hierarchical-clustering) for more infos.
+
+## Issues
+A list of encountered errors and their solution is given [here](https://gitlab.pasteur.fr/gletort/fishfeats/-/wikis/Known-errors-and-solutions)

docs/test.md

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+# test

mkdocs.yml

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+site_name: FishFeats Documentation
+repo_url: https://github.com/gletort/FishFeats/
+
+nav:
+    - Home: home.md
+
+theme:
+    name: material
+    features:
+        - navigation.footer
+    color_mode: dark
+    palette:
+        # Palette toggle for dark mode
+        - media: "(prefers-color-scheme: dark)"
+          scheme: slate
+          primary: white
+          accent: teal
+          toggle:
+            icon: material/lightbulb
+            name: Switch to light mode
+        # Palette toggle for light mode
+        - media: "(prefers-color-scheme: light)"
+          scheme: default
+          primary: white
+          accent: dark blue
+          toggle:
+            icon: material/lightbulb-outline
+            name: Switch to dark mode