Once napari, and the cellfinder plugin is installed, open napari, and load the plugin (
Then load your data (e.g. using the
File-> menu, or by dragging and dropping data). There must be two registered channels, a signal channel (containing fluorescently labelled cells), and a background channel (containing only autofluroescence).
There are many parameters that can be set (see Parameters to set), but the following options must be set before running the plugin
Signal image - set this to the image layer containing the labelled cells
Background image - set this to the image layer without cells
Voxel size (z) - in microns, the plane-spacing (from one 2D section to the next)
Voxel size (y) - in microns, the voxel size in the vertical (top to bottom) dimension
Voxel size (x) - in microns, the voxel size in the horizontal (left to right) dimension
Click the Run button.
The plugin will then run (this may take a while if you're analysing a large dataset), and will produce two additional image layers:
Detected - these are the cell candidates classified as cells
Rejected (hidden by default) - these are the cell candidates classified as artefacts.
The cell coordinates can be saved using any napari plugin (e.g. to csv). To save the cell coodinates in the cellfinder XML format:
Select the points layers (e.g. Detected and Rejected)
Save Selected Layer(s)
.xml extension (e.g.