IdentifyYeastCells (CellProfiler#8)

* identifyyeastcells + tests * %globals to format documentation update, spelling * reformat * remove outline and 2.12 debugging * remove unused imports * visible_settings rename * detach YS from cellprofiler * derive module from ImageSegmentation * move load_image_grayscale * requirements and travis * change import * run CP in headless mode to avoid wx * remove test incompatible with plugin approach * remove reference to centrosome * added cellstar 1.3.0 * option to download zip added to readme * fix invalid precision translation * increase default seeds parameters * conversion for previous versions * revert adding requirements with cellstar * _help fix * CP 3.1.8 compatibility
domchom · Jun 27, 2019 · 9a1220c · 9a1220c
1 parent e461ba1
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diff --git a/.gitignore b/.gitignore
@@ -33,6 +33,7 @@ nosetests.xml
 .mr.developer.cfg
 .project
 .pydevproject
+.idea
 
 *.egg-info/
 *.iml
@@ -45,4 +46,4 @@ build/
 dist/
 frozen_version.py
 plugins/
-src/
+src/
diff --git a/README.md b/README.md
@@ -13,6 +13,8 @@ Please see help here: https://github.com/CellProfiler/CellProfiler/blob/master/c
     cd PLUGIN_DIRECTORY
     git clone https://github.com/CellProfiler/CellProfiler-plugins.git
     ```
+    
+    Alternatively download zip and manually extract to PLUGIN_DIRECTORY.
 
 1. Install required dependencies:
 	```

diff --git a/cellstar/__init__.py b/cellstar/__init__.py
@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+"""
+CellStar package providing CellStar algorithm for segmentation of yeast cells in brightfield imagery.
+Date: 2013-2016
+Website: http://cellstar-algorithm.org/
+"""
+__author__ = 'Adam Kaczmarek, Filip Mróz, Szymon Stoma'
+__all__ = ["segmentation"]
diff --git a/cellstar/core/__init__.py b/cellstar/core/__init__.py
@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+"""
+Core package including main components used in CellStar segmentation.
+Date: 2013-2016
+Website: http://cellstar-algorithm.org/
+"""
+__all__ = ["image_repo", "point", "seed", "seeder", "snake", "snake_filter"]
diff --git a/cellstar/core/config.py b/cellstar/core/config.py
@@ -0,0 +1,84 @@
+# -*- coding: utf-8 -*-
+"""
+Config is a storage for default CellStar configuration.
+Date: 2013-2016
+Website: http://cellstar-algorithm.org/
+"""
+
+
+def default_config():
+    return {
+        'segmentation': {
+            'foreground': {
+                'FillHolesWithAreaSmallerThan': 2.26,
+                'MaskDilation': 0.136,
+                'MaskMinRadius': 0.34,
+                'MaskThreshold': 0.03,
+                'pickyDetection': False,
+                'blur': 1,
+                'MinCellClusterArea': 0.85
+            },
+            'avgCellDiameter': 35,
+            'background': {
+                'blurSteps': 50,
+                'computeByBlurring': 0.5,
+                'blur': 0.3
+            },
+            'ranking': {
+                'avgInnerBrightnessWeight': 10,
+                'avgBorderBrightnessWeight': 300,
+                'stickingWeight': 60,
+                'shift': 0.68,
+                'maxInnerBrightnessWeight': 10,
+                'logAreaBonus': 18,
+                'maxRank': 100,
+                'avgInnerDarknessWeight': 0
+            },
+            'minArea': 0.07,
+            'cellBorder': {
+                'medianFilter': 0.1
+            },
+            'maxFreeBorder': 0.4,
+            'cellContent': {
+                'MaskThreshold': 0.0,
+                'medianFilter': 0.17,
+                'blur': 0.6
+            },
+            'steps': 2,
+            'maxArea': 2.83,
+            'stars': {
+                'cumBrightnessWeight': 304.45,
+                'maxSize': 1.67,
+                'gradientWeight': 15.482,
+                'sizeWeight': [189.4082],
+                'brightnessWeight': 0.0442,
+                'step': 0.0335,
+                'points': 28,
+                'borderThickness': 0.1,
+                'unstick': 0.3,
+                'backgroundWeight': 0.0,
+                'smoothness': 7.0,
+                'gradientBlur': 0.0
+            },
+            'minAvgInnerDarkness': 0.1,
+            'maxOverlap': 0.3,
+            'seeding': {
+                'from': {
+                    'cellContentRandom': 0,
+                    'cellBorderRemovingCurrSegmentsRandom': 0,
+                    'cellContentRemovingCurrSegments': 1,
+                    'snakesCentroids': 0,
+                    'cellContent': 0,
+                    'cellContentRemovingCurrSegmentsRandom': 0,
+                    'cellBorderRemovingCurrSegments': 0,
+                    'cellBorder': 1,
+                    'snakesCentroidsRandom': 0,
+                    'cellBorderRandom': 0
+                },
+                'ContentBlur': 2,
+                'randomDiskRadius': 0.33,
+                'minDistance': 0.27,
+                'BorderBlur': 2
+            }
+        }
+    }