Comments (7)
Can you try to lower your threshold?
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It didn't help. I just get more unrelated branches but the soma pad error remains.
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@argunsah
Hi, thanks for your interests and reporting this issue. I can confirm the issue and I am looking into it.
I have fixed it by adding the pad and save functions back to the Soma class. Before I commit the updates, do you mind sharing the testing tif?
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also the --soma
flag has been deprecated (I just updated the readme). Now if you add --quality
the tracing function will use the SRET algorithm to reconstruct the soma contour. Otherwise, a simple sphere estimation algorithm will be used.
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The second issue is caused by the pyglet
package we used for the simple rendering function. I currently cannot reproduce this on my side, I guess it was caused by some package version incompatability (rejuvyesh/gym-dmcontrol#1). pyglet is known to be tricky to setup for windows.
I would recommend to drag the result swc file to a software like Vaa3D to render it for now to bypass this problem.
Pls let us know how it goes!
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I tried with --quality option and tried visualizing the .swc using Vaa3D or HBP viewer but didn't see soma. Is this expected?
Another question, if I want to use anisotropic diffusion, what is the option for that? It is not specified in the usage help file.
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If you have --save-soma
and --quality
, the reconstructed soma mask is saved to *.tif.r2.soma.tif in the same folder as your input tif if reconstructed correctly.
For image filtering, there is a script I once implemented under apps/anifilter
that supports the OOF filter and the bi-gaussian filter. It allows the soma to be masked when the image is being filtered.
I have not used this script since we started to use CNNs to preprocess the image and run rivuletpy on the CNN predicted heatmaps. So adventures expected.
$ python anifilter -h
usage: anifilter [-h] -f FILE [-o OUT] [--soma] [--no-soma] [-t THRESHOLD]
[--filtertype FILTERTYPE] [--rlow RLOW] [--rhigh RHIGH]
[--rstep RSTEP] [--rho RHO]
Arguments to perform the anisotropic filter on the input image.
optional arguments:
-h, --help show this help message and exit
-f FILE, --file FILE The input file. A image file (*.tif, *.nii, *.mat).
-o OUT, --out OUT The name of the output file
--soma
--no-soma
-t THRESHOLD, --threshold THRESHOLD
The thresohld to get the segmentation for soma
detection. If not provided, the threshold will be
decided via otsu thresholding (not reliable for noisy
images).
--filtertype FILTERTYPE
The type of filter to use for filtering images (bg or
oof); bf for Bi-Gaussian filter, oof for Optimal
Oriented Flux filter. default: oof
--rlow RLOW The lower bound of radius to try
--rhigh RHIGH The higher bound of radius to try
--rstep RSTEP The step size of trying radius
--rho RHO The rho value for the BG filter. Only used if filter
type is bg
For iterative anisotropic diffusion filter, there is an equavalent plugin in Vaa3D that could be called from commandline Vaa3D Menu->Plug-in->image filters-> anisotropic filter
(not sure if the windows build works)
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Related Issues (18)
- Implement MSFM
- Missing module simpleitk Suggestion: edit instalation instructions HOT 2
- swc.shape and soma.save, soma.pad don't exist HOT 8
- scikit-image<0.14.2 will raise an ImportError with numpy HOT 1
- Setup incompatible with pip3 HOT 2
- Installation documentation error HOT 1
- Get Voxel array HOT 1
- Cannot read .swc file result in NeuroM HOT 2
- Example usage
- Failed to find TIFF header file
- Add V3DRAW support for IO
- ModuleNotFoundError: No module named 'msfm' HOT 1
- Implement new performance metric
- See if dt can be reused from soma detection
- msfm segmentation fault sometimes for Bigneuron first2000 images
- Failed to find TIFF library HOT 16
- setup.py not compatible with pip>10.0.0
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