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DanuserLab / u-probe

Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of the biosensor.
https://pubmed.ncbi.nlm.nih.gov/20235099/
GNU General Public License v3.0
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External segmentation does not work #12

Open gdanuser opened 2 months ago

gdanuser commented 2 months ago

Nicolas tried to segment a cell with an external program (ImageJ) and then loaded the binary masks in the segmentation step. It did not work. Can this be debugged?

gdanuser commented 2 months ago

Bo-Jui and I noted that the registration and the bleed-through tools are non-intuitive. The documentation is not accurate either. We need to meet and work through this. Also, we may want to have other registration options. Instead of bead calibration images we could align the channel masks optimally, in the spirit of what Hanieh does for the zebrafish registration.

gdanuser commented 2 months ago

MSA is very verbose and the auxiliary windows do not close at the end. This gets annoying when the tool is being used for routine analysis.

DanuserLab commented 1 month ago

MSA is very verbose and the auxiliary windows do not close at the end. This gets annoying when the tool is being used for routine analysis.

Thank you for your feedback. The MSA Segmentation step has been modified and a "display output figure" check box was added to the setting GUI of the MSA segmentation. User can use this check box to turn "on" or "off" (default) the auxiliary figures during the execution of the MSA segmentation.