diff --git a/README.md b/README.md index f16a34e5258515fdeced1c341290ae7d5b050ab1..a8e2a67fd17bf6f4eb1f980af67076dda54d9fe6 100755 --- a/README.md +++ b/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).  +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