ChristophKirst ClearMap issues

ChristophKirst / ClearMap

ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.

http://christophkirst.github.io/ClearMap/build/html/index.html

GNU General Public License v3.0

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issues

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Error during Transform point coordinates with 'elastix_input.txt'

#46 kenjp1223 closed 1 year ago
0
ImportError: cannot import name 'Texture3D' from 'vispy.visuals.volume'

#45 camtboyd opened 2 years ago
2
Elastix runtime error

#44 Hesham3esa opened 2 years ago
0
ClearMap can't find my .ilp file for celldetection

#43 bhnrus closed 3 years ago
0
Interfacing Ilastik

#42 bhnrus closed 3 years ago
0
Issue with Installation, setting.py specifically

#41 Artem-ctrl opened 3 years ago
3
findCenterOfMaxima returns non integer center coordinates, which are not valid in voxelizePixel function

#40 pderdeyn opened 3 years ago
0
problems with the Analysis script

#39 km-khan closed 4 years ago
2
Problems with Elastix

#38 enovinbakht opened 4 years ago
2
Two of the Unlabelled regions actually labels parts of two different regions

#37 coelhocao opened 4 years ago
0
no

#36 enovinbakht closed 4 years ago
0
itk::ERROR: RandomCoordinateSampler Please select a smaller SampleRegionSize!

#35 pforai opened 4 years ago
0
Too many files open

#34 Sattlert2 opened 4 years ago
0
annotated counts not registering to csv

#33 aaubry89 closed 4 years ago
0
'OverflowError('cannot serialize a string larger than 2 GiB',)

#32 mkywall opened 4 years ago
0
TIFFReadDirectory warning: Unknown field with tag 50838

#31 mbzkandel opened 4 years ago
1
Python crashes during resampling

#30 aaubry89 closed 5 years ago
0
elastix library not loaded (MacOSX) despite existing in path

#29 aaubry89 closed 5 years ago
1
Region specific heatmaps

#28 keithmurphy opened 5 years ago
2
No module named 'Cython'

#27 aaubry89 closed 5 years ago
8
Anyone tried using the ABA Mouse CCF v3 as Atlas and Annotation files?

#26 auesro opened 5 years ago
7
raise RuntimeError('alignData:

#25 keithmurphy opened 5 years ago
22
sta.colorPvalues Function generates a duplicated stack

#24 auesro closed 5 years ago
1
Anterior blob/wall

#23 sronilsson closed 5 years ago
1
IndexError when callling plt.plotOverlayPoints(data, cells, z = (10,16))

#22 vzickus opened 5 years ago
2
'module' object has no attribute 'FileList' when calling "stat.calculateStatistics"

#21 vzickus opened 5 years ago
0
test annotation data download

#20 crazyhottommy opened 5 years ago
15
TypeError: writeData() got an unexpected keyword argument 'startIndex' when setting "save" option in Cell Detection Parameters

#19 vzickus opened 5 years ago
2
RunTimeError - alignData

#18 basakakdogan closed 5 years ago
1
can't run clearmap

#17 AbsolemPillar opened 5 years ago
6
cells_heatmaps do not match the size of the atlas or resampled images

#16 vzickus closed 5 years ago
1
filterKernel2D indices fix and log filter fix

#15 vzickus opened 5 years ago
0
FilterKernel.filterKernel2D too many indices for array ?

#14 vzickus closed 5 years ago
3
Table generation. Annotation files only have a single entry.

#13 vzickus closed 6 years ago
6
No CommandLine option "-out" given!

#12 vzickus closed 6 years ago
5
ImportError when importing ClearMap.Analysis.VoxelizationCode (Cython 0.25)

#11 djarecka opened 7 years ago
0
Fixes #9

#10 kannanuv opened 7 years ago
0
Need structure order in the annotated cell count CSV file

#9 kannanuv closed 7 years ago
0
BugFix: stats analysis script

#8 kannanuv closed 7 years ago
0
add cython module to setup.py

#7 jennan closed 7 years ago
1
ValueError: setting an array element with a sequence in countPointsInRegions()

#6 pforai closed 7 years ago
2
IO.writeData() returns string

#5 pforai closed 7 years ago
6
IndexError: tuple index out of range in ClearMap.Anlysis.Voxelization.voxelizeSphere()

#4 pforai closed 7 years ago
12
ClearMap hanging when running resampling in XY

#3 pforai closed 7 years ago
1
iDISCO Python Module

#2 pforai closed 7 years ago
5
error importing VoxelizationCode.pyx

#1 mgxd closed 8 years ago
1