3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data.
This napari plugin was generated with copier using the napari-plugin-template.
You can install segment-embryo via pip:
pip install segment-embryo
We will segment the cells of an embryo and count the mRNA spots tagged in another channel per cell.
Drag a tif- or czi-file from your file-browser and drop it into the napari window. The image will opened. The napari-plugin napari-czifile2 is used to open czi-files.
Open the plugin Scale-Tool plugin from the Plugins-menu. Make sure the voxel-size values are set correctly in nm. Correct the values and the unit if necessary and press the Apply to all button.
Close the Scale-Tool plugin plugin and open the Embryo Segmentation-plugin from the Plugins-menu. Select the layer containing the membranes as input image and the layer containing the nuclei as nuclei image. Press the run button and wait until the segmentation is finished. When the segmentation is finished a Labels layer with the result will be added to the layers list.
If the labels need curation, select the labels layer and save it to a tiff-file via the menu File>Save Selected Layers.... Import the saved labels into the Morphonet 2 standalone client, make the corrrections and export the corrected labels to a tiff-file. Open the tiff-file in napari.
Close the Embryo Segmentation plugin, select the layer containing the mRNA-spots and open the Detect FISH spots-plugin from the Plugins-menu. Estimate the spot size in xy and z in ImageJ and enter the values into the corresponding fields. You can either estimate the threshold let the software find a threshold value. Press the detect spots button. Depending on the result you might want to modify the threshold-value and run the plugin again.
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the MIT license, "segment-embryo" is free and open source software
If you encounter any problems, please [file an issue] along with a detailed description.