This repository contains a graphical tool to manually re-annotate volumetric files. The main use case is the correction of the mouse brain annotations based on the Nissl volumetric file from the Allen Institute.

To install annotateCerebellum, run the following command:

pip install -e .

To generate the documentation on the annotate_cerebellum package, run the following command in the docs folder:

make html # for html website

See other options: make

This tool creates a 2D interface on which you can "redraw" the borders of the cerebellar cortex regions. First open the file manual_annotation_correct.py and adapt the different user parameters files (either numpy or nrrd file):

• The nissl_filename should point to the volumetric file containing the Allen Institute nissl experiment.
• The annotation_filename should point to the volumetric file containing the Allen Institute mouse brain region annotations. This file will be modified by the program.
• The hierarchy_filename corresponds to the name of the Allen Institute json file containing the hierarchy of mouse brain regions.
• The output_filename is the name of the file which will contain the modified annotation volume.

To launch the application, just run:

python manual_annotation_correct.py

In the terminal, the list of the cerebellar cortex subregions will be listed with their corresponding number. You will be asked to provide the number of region that you want to correct.

Then, the list of the three main axis to visualize the brain will be listed with their corresponding number. You will be asked to provide the number of axis of the slices that you want to display.

Once the region has been loaded, the following window will open in which you can modify the annotation file you have selected as input.

You can extend this window and use the mouse wheel to zoom on the brain slice image.This window is composed of two parts. The top part corresponds to the drawing toolbox, and the bottom one is the image interface. A coronal slice of the mouse brain showing your region of interest is displayed in the image interface. The annotations of the region of interest appear in color on top of the nissl expression in grey. Regions in red, green, blue correspond respectively to granular layer, molecular layer and fibers. Regions in purple are protected and cannot be modified.You can exit the application by closing the window, all saved changes will be stored in the output file. Several buttons are shown in the upper menu:

• The button allow you to manually change the annotation voxel by voxel. A group (or color) needs to be selected. Just press the mouse left click button and drag your mouse to draw a line.
• The button allow you to revert the changes you make on the annotations. The changes that you saved cannot be reverted. As for the pen button, click and drag your mouse to revert the changes.
• The button allow you to change the group of adjacent voxels belonging to the same group (ie same color). A group (or color) needs to be selected. Just click on one voxel and the algorithm will find the surrounding voxels for you.
• The button allow you to move within the image. You can also use the scrollbars on the side.
• The slice id scrollbar is used to select your coronal slice of interest.
• The group or region buttons (color buttons) allow you to select the group you want to paint on the annotations.
  • red is granular layer
  • green is molecular layer
  • blue is fiber tracts (arbor vitae)
  • black is outside of the brain
• The button allow you to save your changes. Please note that every change not saved will be not stored in the output file. Also, the eraser button will not be able to correct the changes that have been saved.
• The button allow you to undo your last operation. Only one operation can be reverted.