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wiggins-lab / SuperSegger

A completely automated MATLAB-based trainable image cell segmentation, fluorescence quantification and analysis suite, particularly well suited for high-throughput time lapse fluorescence microscopy of in vivo bacterial cells.
GNU General Public License v3.0
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Plotting Fluorescence Histograms #27

Closed showmepuppies closed 5 years ago

showmepuppies commented 5 years ago

In superSeggerViewerGui, when I try to plot "Fluor1 sum" (or Fluor1 mean, Fluor2 sum, Fluor2 mean) I don't get any fluorescence values on the plot (see image below). Segmentation works fine, and the fluorescence is overlayed on the segments correctly.

Bad plot, showing no fluorescence: Fluor1sum

Screenshot showing fluorescence overlayed on segments: view1

What could be causing this issue? All channels are .tif, 8-bit.

stellastyl commented 5 years ago

Did you have 'Fluorescence statistics' set as true when your run SuperSegger? That would cause Supersegger to not calculate any fluorescence measures. You can check one of the 'Cell files' (https://github.com/wiggins-lab/SuperSegger/wiki/The-cell-data-files) it should have fl1 filled with data if the statistics are there. Let me know if this helps. You can also sent us your data and we can take a look.

showmepuppies commented 5 years ago

Yes I did not tick Fluo statistics. Thanks!