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Fix typo #112

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Fix typo #112

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d3b297b
Fix typo
healthonrails Jun 9, 2022
f78f5aa
Fix Failing to import Texture3D issue
healthonrails Jun 22, 2022
8691794
Update watershed import from segmentation
healthonrails Jun 22, 2022
7bbd474
reformat the code and add brain region IDs
healthonrails Jul 11, 2022
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4 changes: 2 additions & 2 deletions ClearMap/Analysis/Measurements/ShapeDetection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ def detect_shape(source, seeds, threshold = None, verbose = False):
mask = source > threshold;

peaks = vox.voxelize(seeds, shape=source.shape, weights=np.arange(1, seeds.shape[0]+1)).array;
shapes = skimage.morphology.watershed(-source, peaks, mask=mask);
shapes = skimage.segmentation.watershed(-source, peaks, mask=mask);
#shapes = watershed_ift(-source.astype('uint16'), peaks);
#shapes[numpy.logical_not(mask)] = 0;

Expand Down Expand Up @@ -170,4 +170,4 @@ def find_intensity(source, label, max_label = None, method = 'sum', verbose = Fa
timer.print_elapsed_time(head='Intensity detection');

return intensities


4 changes: 2 additions & 2 deletions ClearMap/ImageProcessing/Experts/Cells.py
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Expand Up @@ -58,7 +58,7 @@

default_cell_detection_parameter = dict(
#flatfield
iullumination_correction = dict(flatfield = None,
illumination_correction = dict(flatfield = None,
scaling = 'mean'),

#background removal
Expand Down Expand Up @@ -687,4 +687,4 @@ def _test():
import numpy as np
import ClearMap.Visualization.Plot3d as p3d
import ClearMap.Tests.Files as tsf
import ClearMap.ImageProcessing.Experts.Cells as cells
import ClearMap.ImageProcessing.Experts.Cells as cells