@@ -83,7 +83,8 @@ If you click on `Concatenate aligned images` on the plugin interface, the plugin
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@@ -83,7 +83,8 @@ If you click on `Concatenate aligned images` on the plugin interface, the plugin
# Demo/Test
# Demo/Test
To test this plugin, you can use our [demo dataset](./data/demo_input) proposed in this repository or directly on your own dataset.
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
## Steps
The input of the process should be a `.tiff` 3D and temporal stack with one or more channels.
The input of the process should be a `.tiff` 3D and temporal stack with one or more channels.
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@@ -98,23 +99,34 @@ For example, if the name of the environment is `timereg-env`, type: `conda activ
When it's activated, type `napari` to start Napari.
When it's activated, type `napari` to start Napari.
Go to `Plugins>napari-3dtimereg` to start it.
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*`).
The dialog interface appears to let you choose the folder to process (the one containing your data), the neural networks to use (that you can download from this repository [`FiberFromTransMatch.zip`](./networks/)) and the parameters to you want to use (see [options](#options) part for more details).
Press `Ok` to launch it. If you selected the `visible` mode, images will pop up during the process and you can visualize the different steps. Otherwise, you will only get informations of the plugin advancement in the `Log` window.
## Output
At the end of the process, you will get a folder named `aligned` in which all processed stacks will be saved (registered stacks) with the corresponding TrackMate files if you selected the option.
You can see what you can obtain with our [demo dataset](./data/demo_output).
**Running time**: On a standard computer with one GPU, running the plugin on one image take typically around XXX for a movie wit XX Z-slices and XX time frames.
## 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
# License
Distributed under the terms of the [BSD-3] license, "napari-3dtimereg" is free and open source software.
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.](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1).
If you use it, please cite our paper [Sarde et al., 2025](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1).
