update demo

README.md

@@ -90,7 +90,7 @@ If you use the data from the Zenodo repository, the file to use to test this plu
 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.
+It can be for example generated from a [TrackMate](https://imagej.net/plugins/trackmate/) file with the macro [getTimePoints.ijm](./src/napari-3dtimereg/getTimePoints.ijm) proposed in this repository.
 
 
 Activate your python virtual environement in which napari and the plugin are installed.
@@ -100,14 +100,13 @@ 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*`).
+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 `Movie_C_*`). In our example dataset, choose `0` as the reference channel (the red channel that contains the fibers).
 
 ![example screenshot](./imgs/load.png)
 
+Click `Update` to get to the step to choose the [registration parameters](#calculate-temporal-alignement).
 
-
-
-## Parameters
+### 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`
@@ -118,8 +117,12 @@ In [Sarde et al., 2025](https://www.biorxiv.org/content/10.1101/2025.03.13.64301
 * `spline final spacing: 200`
 * `final order: 1`
 
+When the parameters have been selected, the registration will be calculated. 
+This step can take a lot of time depending on your movie size. 
+
+
 ## Output
-At the end of the process, you will get a folder named `aligned` in which all processed stacks will be saved (registered stacks)
+At the end of the process, you will get a folder named `aligned` in which the registered movie will be saved.
 
 
 # License