Generate figures

N.B. A command line tool has not yet been developed. For now, figures can only be generated by using the --figures flag in cellfinder_run.

By default, if you use the --figures flag, a number of files will be generated. Until custom figures can be generated in cellfinder, these files are generated to allow you to more easily make figures in e.g. FIJI. More details can be found here.

The idea is that these images can be combined to generate more custom figures. These images are all saved in the same coordinate space as the downsampled raw data saved into output_directory/registration. Currently three files will be generated by default.

  • heatmap.nii - This is a 3D histogram, showing cell densities throughout the brain. Likely to be more useful than visualising cell positions for dense areas. By default, this is smoothed, and masked (so that the smoothing doesn’t “bleed” outside of the brain)

  • glass_brain.nii This is a binary image, just showing the brain surface. Plotting this in 3D along with heatmap.nii gives a nice sense of cell density throughout the brain. ClearVolume works well for this.

  • boundaries.nii Another binary image, but showing the divisions between each region in the atlas. More useful for smaller, 3D figures to delineate region boundaries. Also useful to assess registration by overlaying on the raw, downsampled data.

There are not yet many options, but the current options are here:

  • --no-heatmap Don’t generate a heatmap of cell locations

  • --heatmap-bin Heatmap bin size (mm of each edge of histogram cube)

  • --heatmap-smoothing Gaussian smoothing sigma, in mm.

  • --no-outlines Don’t generate outlines of segmentation regions (for overlay)

  • --no-mask-figs Don’t mask the figures (removing any areas outside the brain, from e.g. smoothing)