scaffolding

.gitignore

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+*.egg-info/
+*.iml
+*.pyc
+.cache/
+.eggs/
+.idea/
+.python-version
+build/
+dist/

.travis.yml

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+cache:
+  apt: true
+  directories:
+    - $HOME/.cache/pip
+language: python
+notifications:
+  email: false
+python:
+  - 2.7
+sudo: false
+virtualenv:
+  system_site_packages: true
+script:
+  - python setup.py test -a -x

README.rst

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+# CellStar

cellstar/__init__.py

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+# -*- 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'

cellstar/config/__init__.py

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+# -*- coding: utf-8 -*-
+__author__ = 'Adam Kaczmarek, Filip Mróz'

cellstar/config/config.py

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+# -*- coding: utf-8 -*-
+__author__ = 'Adam Kaczmarek, Filip Mróz'
+
+
+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': 241.319005997,
+                'maxSize': 1.67,
+                'gradientWeight': -92.0672006787,
+                'sizeWeight': [1071.7792126066715],
+                'brightnessWeight': 487.56705379,
+                'step': 0.0335,
+                'points': 28,
+                'borderThickness': 0.1,
+                'unstick': 0.3,
+                'backgroundWeight': 0.0,
+                'smoothness': 9.59491685094,
+                'contentWeight': 0.0,
+                '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
+            }
+        }
+    }

cellstar/core/__init__.py

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+# -*- 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"]