Visualisation

To display the results of cellfinder

These features may not be backwards compatible with old versions of amap and cellfinder. It will also not work if cells have been detected from more than one channel.

For now, this tool depends on amap. Please run pip install amap and then amap_download before running this tool if you don't already have cellfinder installed

cellfinder (and amap) come with a tool for visualising (and editing) results. To launch the viewer, run:

cellfinder_view

A napari window will then open with two options (Load cellfinder project and Load amap project):

Starting screen for the viewer

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.

Data loading buttons

The buttons that appear will vary depending on the data that you have (i.e. if you haven't run registration, that button won't appear).

Be careful which data you load, as it may use a lot of RAM.

Loading data:

  • 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 .tif or .nii.

  • Load downsampled data Load the downsampled data channels from the registration step (usually the fastest approach).

Adding results:

  • 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.

Each part of the dataset will be loaded a "layer" which can be hidden, adjusted and reordered using the boxes on the left hand side. See the napari tutorials for how to navigate the viewer.

zoomed in view showing registration and cell detection results

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