Detecting cells in 3D with cellfinder#
The aim of this tutorial is to get cell detection up and running. The image we use here is very small and has some artefacts. The results are not very good, but it should be enough to see the plugin working! When using cellfinder on your own data, there are many parameters that can be adjusted, and cellfinder will need to be retrained for optimal performance. For more information, please see the full cellfinder documentation.
You will need
napari installed on your computer - please follow
napari’s installation instructions to do so
(including their recommendation to use a
Plugins > Install/Uninstall pluginsand searching for
cellfinder-napariin the searchbox. If it is not installed yet, click on the
This may take a while due to the various dependencies being installed.
On Silicon Macs you may have to run
conda install hdf5 on the command line (in your conda environment) first for the installation to be successful.
Open the cell detection widget by selecting
Plugins > cellfinder-napari > Cell detectionin the napari menu bar near the top left of the window.
The cell detection widget appears on the right-hand side of the window.
Load some sample data
File > Open sample > Sample data (cellfinder-napari). This will open a small two-channel 3D image.
Voxel size (z)is set to
Voxel size (y)is set to
Voxel size (x)is set to
Run(you may need to scroll down)
Detected cells are highlighted by yellow circles.
Ensure that the
Detectedlayer is highlighted
Save the detected cells by clicking
File > Save selected layer(s), choosing a directory and a filename ending in
For more information about how to use the detection plugin to detect cells in your own data, please see the full cell detection guide.