cellfinder (and amap) come with a tool for visualising (and editing) results. To launch the viewer, run:
A napari window will then open with two options (
Load cellfinder project and
Load amap project):
If you have run cellfinder, click
Load cellfinder project and choose the directory set as the output folder. Alternatively, if you only want to inspect the registration, click
Load amap project and choose either an amap output folder, or the
registration directory of a cellfinder project.
Once a project has loaded, a number of buttons will appear on the right hand side of the window.
Load data directory Load raw data as a directory of image files (one image per plane)
Load single image Load raw data as a single multiplane image (e.g. multiplane
Load downsampled data Load the downsampled data channels from the registration step (usually the fastest approach).
Load registration Loads the results of the registration including:
Annotations - image color coded by brain region. When this layer is highlighted (using the panel on the left hand side), you can hover the mouse over each brain region, and see its label in the bottom right hand side.
Boundaries - binary labels of the boundary of each brain region
Load cells Loads the results of cell classification, including the cell candidates classified as cells, and those classified as non-cells. Once cells are loaded, a
Save cells button will appear. If you add or delete cells (using the buttons at the top left), clicking this button will update the
cell_classification.xml file. Be careful, as this will overwrite the existing file.