From c4c7bd9d0dde2d6bf10cd345d2e41bca58162dd7 Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Sun, 9 Jan 2022 11:17:30 +0800
Subject: [PATCH 1/4] Fix blob segmentation to use updated Scikit-image
 watershed function location

Fixes #91. Change the location of `watershed` from the `morphology` to the `segmentation` package in Scikit-image now that the function was removed from the former in Scikit-image v0.19. Also, remove unused import.
---
 magmap/cv/segmenter.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/magmap/cv/segmenter.py b/magmap/cv/segmenter.py
index 1ca50a594..64b586154 100644
--- a/magmap/cv/segmenter.py
+++ b/magmap/cv/segmenter.py
@@ -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
 
@@ -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
 

From 6e7f2b7659ce87fa23f4c2ff136a3d8d4e7b124b Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Mon, 10 Jan 2022 10:58:04 +0800
Subject: [PATCH 2/4] Clarify ROI Editor options' tooltip

Indicate which images the options change.
---
 magmap/gui/visualizer.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/magmap/gui/visualizer.py b/magmap/gui/visualizer.py
index 1653d4c45..14e8123ac 100644
--- a/magmap/gui/visualizer.py
+++ b/magmap/gui/visualizer.py
@@ -442,11 +442,11 @@ 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

From f89292d04975945ed3776194d6022b1a3b10deda Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Mon, 10 Jan 2022 11:00:00 +0800
Subject: [PATCH 3/4] Clarify the scale detections control

As indicated in #87, the "Scale detections" control label is confusing since it does not operate on the ROI Editor but only on the 3D viewer. Rename this control and add a tooltip to clarify this behavior.
---
 magmap/gui/visualizer.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/magmap/gui/visualizer.py b/magmap/gui/visualizer.py
index 14e8123ac..9bdde49ff 100644
--- a/magmap/gui/visualizer.py
+++ b/magmap/gui/visualizer.py
@@ -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
@@ -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",

From 06e1d955d827d23a2cbd45b4c8d173d65960c72d Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Mon, 10 Jan 2022 11:12:25 +0800
Subject: [PATCH 4/4] Changelog entry for fixed blob segmentations

---
 docs/release/release_v1.6.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/release/release_v1.6.md b/docs/release/release_v1.6.md
index 68bf4fb80..4e6b4c0bb 100644
--- a/docs/release/release_v1.6.md
+++ b/docs/release/release_v1.6.md
@@ -23,6 +23,8 @@
 
 #### Cell detection
 
+- Fixed blob segmentation for newer versions of Scikit-image (#91)
+
 #### Volumetric image processing
 
 #### I/O