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manually-segment-brain-regions.md

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Manually segment brain regions

To manually segment brain regions in standard space that can then be visualised along with other samples (e.g. in BrainRender.)

N.B. This tool depends (for now) on amap. Please run pip install amap and then amap_download before running this tool if you don't already have cellfinder installed

Prerequisites

Data must be registered to a standard atlas (currently only the Allen Reference Atlas is supported) using amap (or the amap based registration in cellfinder). Please follow the instructions for these packages, and ensure that the channel that you want to segment is downsampled (e.g. using the --downsample flag in amap).

Usage

Command line

    manual_region_seg "name_of_downsampled_image.nii" registration_directory

Arguments

Run manual_region_seg -h to see all options.

Positional arguments

  • Downsampled image to be segmented, as a string (e.g. "downsampled.nii")

  • amap/cellfinder registration directory (e.g.

    /home/analysis/cellfinder_output/registration/)

The following options may also be used:

  • --preview Preview the segmented regions in brainrender (default:False)

  • --volumes Calculate the volume of each brain area included in the

    segmented region

  • --summarise Summarise each region (centers, volumes etc.)

  • --shading Object shading type for brainrender (flat, giroud or phong). Default: flat

  • --alpha Object transparency for brainrender

  • --brush-size Default size of the label brush.

napari GUI

manual_region_seg will transform your image into standard space (this may take a few minutes) and then display the image in a napari viewer:

manual_seg_window

To segment regions:

  • Ensure that the "new_region" tab is selected (left hand side)

  • Rename this region (by selecting the "new_region" text)

  • Navigate to where you want to draw your region of interest.

    • Use the scroll bar at the bottom (or left/right keys) to navigate

      through the image stack

    • Use the mouse scrollwheel to zoom in or out

    • Drag with the mouse the pan the view

  • Choose a brush size (top left box)

  • Activate painting mode (by selecting the paintbrush, top left). You can

    go back to the navigation mode by selecting the magnifying glass.

  • Colour in your region that you want to segment, ensuring that you make a

    solid object.

  • Selecting the ndim toggle in the top left will extend the brush size in three dimensions (so it will colour in multiple layers).

  • To add a new region press Control+N

  • Repeat above for each region you wish to segment.

  • Press Alt-Q on your keyboard to save the regions. If you used the --preview flag, once they are saved, they will be displayed in a brainrender window.

Editing regions:

If you have already run manual_region_seg, and run it again, the segmented regions will be shown. You can edit them, and press Control+S to resave them. If you don't want to save any changes, press Control+X to exit. The regions will still be previewed if you have selected that option.