Removal of spurious pixels (#349)

* Removal of spurious pixelsn

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* minor simplification of spurious pixel removal code

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove debug print statement

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: alessandrofelder <[email protected]>
Co-authored-by: Alessandro Felder <[email protected]>

brainglobe_atlasapi/atlas_generation/atlas_scripts/axolotl_atlas.py

@@ -9,6 +9,7 @@
 import pooch
 from brainglobe_utils.IO.image import load_nii
 from rich.progress import track
+from skimage.measure import label, regionprops
 
 from brainglobe_atlasapi import utils
 from brainglobe_atlasapi.atlas_generation.mesh_utils import (
@@ -74,6 +75,21 @@ def create_atlas(working_dir, resolution):
  reference_image = (reference_image - dmin) * dscale
  reference_image = reference_image.astype(np.uint16)
 
+ # mask: put 1 where there is an annotation
+ annotation_mask = np.zeros(annotation_image.shape)
+ annotation_mask[annotation_image > 0] = 1
+
+ # find the connected regions in the mask
+ labeled_image = label(annotation_mask)
+ regions = regionprops(labeled_image)
+
+ # find the pixels belonging to the largest region
+ largest_region = max(regions, key=lambda region: region.area)
+ largest_mask = labeled_image == largest_region.label
+
+ # keep only annotations in the largest connected region
+ annotation_image = annotation_image * largest_mask
+
  hierarchy = []
 
  # create dictionaries # create dictionary from data read from the CSV file