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klasma / BaxterAlgorithms

Software for segmentation, tracking and analysis of cells in microscope image sequences.
MIT License
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Ground Truth export on 3D dataset #9

Open BennyGinger opened 4 years ago

BennyGinger commented 4 years ago

Hi,

I've been trying to export segmentation and tracking ground truths of a dataset that is composed of 121 frames and 31 slices per frame, on a deployed windows version of the software and I always gets that message:

Error using writetif (line 40) Writing TIFFs with 31 components is not supported with IMWRITE. Use Tiff instead. Type "help Tiff" for more information.

Error in imwrite (line 485)

Error in SaveSEGGT (line 57)

Error in CTCExportGUI/ExportCallback (line 99)

Error using pause (line 20) Error while evaluating UIControl Callback.

Thanks for your help. Ben

klasma commented 4 years ago

Hi Ben,

Sorry for the late response. Now I have taken a look at this. It was not possible to export segmentation ground truths in 3D. That was a bug. I have now fixed it on the master branch, but I have not yet deployed a new version.

It seems to be possible to export tracking ground truths. If you do not have a Matlab license, you could actually export a tracking ground truth and rename the files, because the images are 16-bit label images in both cases. Some labels will most likely be missing in each frame. That does not affect the SEG measure in my implementation but I don't know how the measure is implemented in the software provided by the organizers.

The 3D ground truths are exported to full z-stacks and not individual z-slices. In the cell tracking challenges, the Fluo-N3DH-SIM+ dataset has full z-stacks in the ground truth but all other datasets have individual z-slices. That means that all z-slices must be segmented but you don't have to segment all frames. In the future, I will try to add support for individual z-slices, but that will require a little more work. If you need individual z-slices, you could write your own script in Matlab, Python or something else to convert to that format.

Best regards, Klas

On Fri, Apr 10, 2020 at 3:21 PM BennyGinger notifications@github.com wrote:

Hi,

I've been trying to export segmentation and tracking ground truths of a dataset that is composed of 121 frames and 31 slices per frame, on a deployed windows version of the software and I always gets that message:

Error using writetif (line 40) Writing TIFFs with 31 components is not supported with IMWRITE. Use Tiff instead. Type "help Tiff" for more information.

Error in imwrite (line 485)

Error in SaveSEGGT (line 57)

Error in CTCExportGUI/ExportCallback (line 99)

Error using pause (line 20) Error while evaluating UIControl Callback.

Thanks for your help. Ben

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BennyGinger commented 4 years ago

Thanks a lot Klas.

I've tried the tracking ground Truth and it worked! I will wait for the update then for the segmentation.

Once again, thanks, Ben