Merge branch 'main' of https://gitlab.pasteur.fr/gletort/napari-3dtimereg into main

README.md

@@ -10,9 +10,28 @@ Temporal registration of 2D/3D movies on one channel based on [itk-elastix](http
 Adaptated from [multireg](https://gitlab.pasteur.fr/gletort/multireg) for temporal movies.
 For a tutorial on using `elastix` for registration, see [this tutorial](https://m-albert.github.io/elastix_tutorial/intro.html).
 
+* [Installation](#installation)
+    * [System requirement](#system-requirement)
+    * [Installation steps](#installation-steps)
+* [Usage](#usage)
+* [Demo](#demotest)
+* [License](#license)
 
 ----------------------------------
-## Installation
+# Installation
+
+
+## System requirement
+
+`napari-3dtimereg` is a Napari plugin therefore can be installed on all operating systems. 
+It requires a python environement compatible with `Napari` and `elastix` version.
+
+### Tested system
+It has been tested on python 3.9, napari XX and elastix XX.
+
+## Installation steps
+
+In a python environment that contains Napari:
 
 * You can install the plugin directly in `Napari` by going to `Plugins>Install/Uninstall plugins` and search for `napari-3dtimereg`
 
@@ -21,7 +40,10 @@ For a tutorial on using `elastix` for registration, see [this tutorial](https://
     pip install napari-3dtimereg
 
 
-## Usage
+If you don't have Napari installed yet, see [here](https://napari.org/stable/tutorials/fundamentals/quick_start.html#napari-quick-start) for installation instructions.
+
+
+# Usage
 
 You can launch `3dtimereg` in napari by going to `Plugins>Do 3D movie registration (napari-3dtimereg)`.
 
@@ -58,9 +80,53 @@ When all frames have been processed, each color chanel and each frame have been
 
 If you click on `Concatenate aligned images` on the plugin interface, the plugin will create a single composite movie from the aligned images, save it and delete the separated images in the `aligned` folder. 
 
-## License
 
-Distributed under the terms of the [BSD-3] license, "napari-3dtimereg" is free and open source software
+# Demo/Test
+
+To test this plugin, you can use our [demo dataset](https://zenodo.org/records/15028169) proposed in a Zenodo repository or directly on your own dataset.
+If you use the data from the Zenodo repository, the file to use to test this plugin is the movie `Registration_WTn1_Crop_V1.tif` which has been cropped from our dataset to reduce the size.
+
+## Steps
+The input of the process should be a `.tiff` 3D and temporal stack with one or more channels. 
+If you want to use fix points registration option, you should have a file that contains the position of each tracked point at each time.
+See in our demo dataset for the format of this file.
+It can be for example generated from a [TrackMate](https://imagej.net/plugins/trackmate/) file with the macro [getTrackPosition](XX) proposed in this repository.
+
+
+Activate your python virtual environement in which napari and the plugin are installed.
+For example, if the name of the environment is `timereg-env`, type: `conda activate timereg-env`.
+
+When it's activated, type `napari` to start Napari. 
+Go to `Plugins>napari-3dtimereg` to start it.
+
+Load the movie to register. The plugin will ask you to choose the channel on which to calculate the registration, so choose a channel that should be immobile during the movie (for example, the channel containing the fibers which should be stable over time).
+Set the `reference channel` to the corresponding channel number (that you can see in the bottom left part of the viewer, with the layers name `MovieChannel*`).
+
+![example screenshot](./imgs/load.png)
+
+
+
+
+## Parameters
+
+In [Sarde et al., 2025](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1), we used the following parameter values to register our intravital movies:
+* `use reference points: True`
+* `rigid resolution: 4`
+* `spline resolution: 2`
+* `iterations: 1000`
+* `rigid final spacing: 50`
+* `spline final spacing: 200`
+* `final order: 1`
+
+## Output
+At the end of the process, you will get a folder named `aligned` in which all processed stacks will be saved (registered stacks)
+
+
+# License
+
+Distributed under the terms of the [BSD-3] license, "napari-3dtimereg" is free and open source software.
+
+If you use it, please cite our paper [Sarde et al., 2025](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1). 
 
 
 [napari]: https://github.com/napari/napari