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Multi cell segmentation in RW #284

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CellDynamics opened this issue Dec 20, 2017 · 0 comments
Closed

Multi cell segmentation in RW #284

CellDynamics opened this issue Dec 20, 2017 · 0 comments
Labels
C: QuimP-RandomW feature P: major
Projects
QuimP
Milestone
v18.01.01

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@CellDynamics
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Treat cell separately to improve results when cells touch each other.
@CellDynamics CellDynamics added this to the Next iteration milestone Jan 3, 2018
@CellDynamics CellDynamics added this to In progress in QuimP Jan 3, 2018
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Changed storage for seed maps to modified HashMap.
ee917a4 
Accept multiple maps for one type of seeds.

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added maps
73e880a 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Solver process only fg maps
00a7f32 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Support for multicell in most of RW internal methods
b7d279e 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Set bck iter number dependent on fg
31009f5 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Propagate seeds supports muticolor images
caf05af 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Fixed decodeSeeds
f3eb7cc 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Tests for multi color seeds and some todos
042e010 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Verified multi seed segmentation
9cdfc4c 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added simple UI for selecting seeds by ROIs. New TODOs
da8b51e 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Refactored and cleaned seeds
54e8b5e 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Reworked SeedPicker
198b182 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Changed UI
925cf57 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added conversion from grayscale to Seeds
f425b53 
Task: #284
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Changes in UI
9281e9e 
Task: #284
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added exception on empty roi seeds
6ca48ce 
Task: #284
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Almost finished
d865646 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Adapted Morphological processor to grayscale images.
27103b2 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Fixed RW algorithm, wrong concatenation of BCK
aa65300 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Updated for masks
eae303a 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added exception for converter from grayscale image
83e2f67 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Added mask from Qconf preview
b66cb11 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
baniuk pushed a commit that referenced this issue Jan 9, 2018
@CellDynamics
Exception handling in show seeds and better text wrapping
b30a75f 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Renamed test method
1112099 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Updated TrackOutline to return also color of original object.
8c7d4f4 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Updated contour scaling to preserve groups of objects across color
7f2ce93 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Updated tests and fixed issue in getComposite
7b0b904 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Fixed Qconf
14be502 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Comment
74c2698 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Added structures for holding grayscale maps.
c4aa3b7 
Introduced seed maps and probability maps and rewritten core processors
to support them.

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Comments

Changed storage for seed maps to modified HashMap.

Accept multiple maps for one type of seeds.

Added maps

Solver process only fg maps

Support for multicell in most of RW internal methods

Set bck iter number dependent on fg

Propagate seeds supports muticolor images

Fixed decodeSeeds

Tests for multi color seeds and some todos

Verified multi seed segmentation

Added simple UI for selecting seeds by ROIs. New TODOs

Refactored and cleaned seeds
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Added seed picker tool and improved Seeds structure
3e6211a 
Adapted RW UI for grayscale support.

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Reworked SeedPicker

Changed UI

Added conversion to stack and grayscale image.

Task: #239

Added conversion from grayscale to Seeds

Task: #284

Changes in UI

Task: #284

Added exception on empty roi seeds

Task: #284

Almost finished
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Updated GenerateMAsk for grayscale images
5180a89 
Fixed bugs in mask processing in RW and SeedPropagator

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Adapted Morphological processor to grayscale images.

Updated GenerateMAsk to support grayscale images

Fixed RW algorithm, wrong concatenation of BCK

Updated for masks

Added exception for converter from grayscale image

Added mask from Qconf preview

Exception handling in show seeds and better text wrapping
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Updated TrackOutline to return color of tracked objects.
993adf1 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Updated comments

Renamed test method

Updated TrackOutline to return also color of original object.
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Contour scaling preserves groups of objects.
5b25146 
Fixes also other issues.

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Updated contour scaling to preserve groups of objects across color

Updated tests and fixed issue in getComposite

Fixed Qconf

Comment
CellDynamics added a commit that referenced this issue Jan 10, 2018
@CellDynamics
Contour scaling preserves groups of objects.
aa4a9ad 
Fixes also other issues.

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
Updated contour scaling to preserve groups of objects across color

Updated tests and fixed issue in getComposite

Fixed Qconf

Comment
CellDynamics added a commit that referenced this issue Jan 11, 2018
@CellDynamics
Added show mask button
f6c7adf 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 11, 2018
@CellDynamics
Added info about loaded ROIs
0cecffe 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 11, 2018
@CellDynamics
Protection against the same seed and input image.
7c68c7c 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 11, 2018
@CellDynamics
Add return prob maps for last frame. Name refactoring
fe07d37 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 11, 2018
@CellDynamics
Tests and fixed order of show commands actions
71b1a30 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 12, 2018
@CellDynamics
Added debug routines
c53dca4 
Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
CellDynamics added a commit that referenced this issue Jan 15, 2018
@CellDynamics
Changed Dummy seed propagator to not produce BG if not present
8377c99 
Also many null pointer bugs fixed

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)
@CellDynamics CellDynamics moved this from In progress to Done in QuimP Jan 16, 2018
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Labels
C: QuimP-RandomW feature P: major
Projects
QuimP
  
Done
Milestone
v18.01.01
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@CellDynamics