MATLAB GUI#

Note

Interactive GUI - please run each section individually. DO NOT run the entire script at once.

initial_alignment#

For loading path and image information:

  • Path setup (first section): Users need to modify the paths to match their system

  • Image sizing: It’s recommended to resize images first: - 800 × 1140 pixels for coronal view - 1320 × 800 pixels for sagittal view

  • If using original size images, specify use_already_downsampled_image=false in slice_preprocessing.m and ensure my_Resolution is set correctly

slice_preprocessing#

Image preprocessing pipeline including:

  • Cropping and rotation

  • Contrast adjustment

  • Downsampling of histology images

slice_registration#

Slice registration to Allen Brain Atlas

Tip

Interactive Registration Workflow:

  • Setting transform points: Press t in both slice and atlas viewer windows to label transformation points (minimum 10 points recommended)

  • View results: Press h + a to see the registration overlay

  • Load existing transforms: Press l to load transformation matrix

After each image:

  • Press d to delete all points in both windows

  • Press h to leave overlay of current slice in atlas window

  • Press → (right arrow) in slice window for next image

  • Press ↓ (down arrow), then scroll to find corresponding atlas position

  • Label new transformation points for the current image

Applying existing transformation matrices:

  • Copy the .mat transformation file to the appropriate directory

  • Press l to load, then x to save the transformed image

  • Verify result using h + a

save_transform_mat#

Save the 3×3 transformation matrix for batch processing

analysis_rois#

Analyze pixel-wise ROI locations and extract spatial coordinates within the Allen Brain Atlas coordinate system