diff --git a/README.md b/README.md index 244a447be8f6e38abefb29277f1794e552e224b3..f16a34e5258515fdeced1c341290ae7d5b050ab1 100755 --- a/README.md +++ b/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*`). + + + + + + +## 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