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Fix blob segmentation #92

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merged 4 commits into from
Jan 12, 2022
Merged

Fix blob segmentation #92

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c4c7bd9
Fix blob segmentation to use updated Scikit-image watershed function …
yoda-vid Jan 9, 2022
6e7f2b7
Clarify ROI Editor options' tooltip
yoda-vid Jan 10, 2022
f89292d
Clarify the scale detections control
yoda-vid Jan 10, 2022
06e1d95
Changelog entry for fixed blob segmentations
yoda-vid Jan 10, 2022
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2 changes: 2 additions & 0 deletions docs/release/release_v1.6.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@

#### Cell detection

- Fixed blob segmentation for newer versions of Scikit-image (#91)

#### Volumetric image processing

#### I/O
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3 changes: 1 addition & 2 deletions magmap/cv/segmenter.py
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Expand Up @@ -3,7 +3,6 @@
"""Segment regions based on blobs, labels, and underlying features.
"""

from multiprocessing import sharedctypes
from time import time
from typing import Any, List, Optional, Tuple, Union

Expand Down Expand Up @@ -626,7 +625,7 @@ def watershed_distance(foreground, markers=None, num_peaks=np.inf,
local_max = feature.peak_local_max(
distance, indices=False, num_peaks=num_peaks)
markers = measure.label(local_max)
watershed = morphology.watershed(
watershed = segmentation.watershed(
-distance, markers, compactness=compactness, mask=mask)
return watershed

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16 changes: 9 additions & 7 deletions magmap/gui/visualizer.py
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Expand Up @@ -322,7 +322,9 @@ class Visualization(HasTraits):
_segs_moved = [] # orig seg of moved blobs to track for deletion
_scale_detections_low = 0.0
_scale_detections_high = Float # needs to be trait to dynamically update
scale_detections = Float
scale_detections = Float(
tooltip="Change the size of blobs in the 3D viewer"
)
segs_pts = None
segs_selected = List # indices
# multi-select to allow updating with a list, but segment updater keeps
Expand Down Expand Up @@ -442,11 +444,11 @@ class Visualization(HasTraits):
"Panes: show back and top panes\n"
"Shadows: show blob shadows as circles")
_check_list_2d = List(
tooltip="Filtered: show filtered image after detection\n"
"Border: margin around ROIs\n"
"Seg: segment blobs\n"
"Grid: overlay a grid\n"
"MIP: maximum intensity projection")
tooltip="Filtered: show filtered image after detection in ROI planes\n"
"Border: margin around ROI planes\n"
"Seg: segment blobs during detection in ROI planes\n"
"Grid: overlay a grid in ROI planes\n"
"MIP: maximum intensity projection in overview images")
_DEFAULTS_2D = [
"Filtered", "Border", "Seg", "Grid", "MIP"]
_planes_2d = List
Expand Down Expand Up @@ -624,7 +626,7 @@ class Visualization(HasTraits):
values=[e.value for e in BlobColorStyles],
format_func=lambda x: x)),
),
Item("scale_detections",
Item("scale_detections", label="Scale 3D blobs",
editor=RangeEditor(
low_name="_scale_detections_low",
high_name="_scale_detections_high",
Expand Down