Merge pull request #101 from BioimageAnalysisCoreWEHI/add_napari_docs

Add docs for napari plugin
BioimageAnalysisCoreWEHI · Jan 31, 2025 · 413c4b6 · 413c4b6
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diff --git a/docs/images/001_start_plugin.png b/docs/images/001_start_plugin.png
diff --git a/docs/images/002_plugin.png b/docs/images/002_plugin.png
diff --git a/docs/images/003_open_image.png b/docs/images/003_open_image.png
diff --git a/docs/images/004_configure.png b/docs/images/004_configure.png
diff --git a/docs/images/005_deskewed.png b/docs/images/005_deskewed.png
diff --git a/docs/images/deskew_active.png b/docs/images/deskew_active.png
diff --git a/docs/images/green_tick.png b/docs/images/green_tick.png
diff --git a/docs/images/plugin_tabs.png b/docs/images/plugin_tabs.png
diff --git a/docs/napari_plugin.md b/docs/napari_plugin.md
@@ -0,0 +1,61 @@
+# Napari Plugin
+
+## Starting the plugin
+
+The napari plugin has been redesigned in the newer version.
+To activate the plugin, activate the `napari-lattice` environment in your terminal and type `napari` in the console.
+The plugin is under `Lattice Lightsheet Analysis`
+
+![Activate plugin](./images/001_start_plugin.png){ width="600" }
+
+The plugin should appear on the right side. You may have to resize the window.
+
+![llsz_plugin](./images/002_plugin.png){ width="600" }
+
+The functionalities with napari-lattice have been separated out into tabs:
+
+![plugin_tabs](./images/plugin_tabs.png){ width="600" }
+
+If its configured correctly, you should see a green tick next to the tab name, else you will see a red cross.
+
+![green_tick](./images/green_tick.png)
+
+To load an image, drag and drop it into napari. You can get some sample data [here](https://zenodo.org/records/7117784). We are using `RBC_tiny.czi` as an example here.
+
+![open_image](./images/003_open_image.png){ width="600" }
+
+## Configuration
+
+To configure any parameters, you can change the settings here:
+
+![settings](./images/004_configure.png)
+
+## Deskewing
+
+To use the specific image for processing, you will have to select it under the `Image Layer(s) to Deskew` box on the right. Here, we will click on `RBC_tiny`. As its a czi file it should read the `metadata` accordingly and you will see a green tick.
+
+![deskew_active](./images/deskew_active.png)
+
+If you are loading a czi, the metadata fields should be populated automatically.
+
+To `Preview` the deskewed image, click `Preview` and choose the appropriate `channel` and `time`.
+
+You should see the deskewed image appear as an extra layer with the `Preview` suffix attached to it.
+
+![deskewed](./images/005_deskewed.png){ width="600" }
+
+??? Extra_info
+    If you look at the terminal after deskew, you should see the settings used and any other metadata associated with the dataset. It is handy for troubleshooting.
+
+More instructions to be added...
+
+## Deconvolution
+
+## Cropping
+
+## Workflow
+
+## Output (Saving files)
+
+
+
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Napari Lattice
+site_name: napari_lattice
 
 markdown_extensions:
 - mkdocs-click
@@ -7,10 +7,14 @@ markdown_extensions:
 - pymdownx.superfences 
 - admonition
 - pymdownx.details
+- attr_list
+- md_in_html
+- pymdownx.blocks.caption
 
 nav:
 - index.md
 - installation.md
+- napari_plugin.md
 - cli.md
 - api.md
 - workflow.md

diff --git a/resources/LLSZ_window.png b/resources/LLSZ_window.png
diff --git a/resources/crop&deskew_active.png b/resources/crop&deskew_active.png
diff --git a/resources/crop&deskew_initial.png b/resources/crop&deskew_initial.png
diff --git a/resources/deconvolution.png b/resources/deconvolution.png
diff --git a/resources/installation.jpg b/resources/installation.jpg
diff --git a/resources/plugin_installation.png b/resources/plugin_installation.png
diff --git a/resources/preview_deskew.png b/resources/preview_deskew.png
diff --git a/resources/workflow.png b/resources/workflow.png