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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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Not opening : Delete dust, bubbles and other bad regions #1

Closed mxardre closed 7 years ago

mxardre commented 7 years ago

Hi, I am trying to use this amazing tool. To do so I follow the instructions there : https://github.com/wiggins-lab/SuperSegger/wiki/Creating-your-own-constants-file However when I want to train the software I do not manage to go from Providing the algorithm with examples to Delete dust, bubbles and other bad regions. The window to delete dust and bubble does not open. When a start the segmentation I got a warning : 

Warning: File '~/Desktop/training/phase/xy1/phase/xy1/seg/.trackOptiStripSmall-Step1.mat' not found. 
> In cleanSuperSegger (line 46)
  In BatchSuperSeggerOpti>intProcessXY (line 308)
  In parallel_function (line 476)
  In BatchSuperSeggerOpti (line 212)
  In trainingGui>cut_and_seg_Callback (line 129)
  In gui_mainfcn (line 95)
  In trainingGui (line 39)
  In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)trainingGui('cut_and_seg_Callback',hObject,eventdata,guidata(hObject))

And then the window "Training new segmentation constant" is reset.

Any idea? Im running on mac osx 10.10.5, matlab R2016b

stellastyl commented 7 years ago

The warning is totally fine - it should not stop the program. Did it stop at that point? I would be happy to look into it if you send me 5-10 of the pictures you were using. I did fix a couple of things recently, could you please download the newest version of SuperSegger and try it again? Just to make sure this wasn't from an older version!

Thank you!

mxardre commented 7 years ago

Hi,Thanks a lot! I can show you with a google hangout if you would like. I don't know what time it is for you (23h for me). It is possible for me in 1h20.Maxime

-------- Message d'origine -------- De : Stella notifications@github.com Date : 23/01/2017 21:41 (GMT+01:00) À : wiggins-lab/SuperSegger SuperSegger@noreply.github.com Cc : mxardre maxime.ardre+git@gmail.com, Author author@noreply.github.com Objet : Re: [wiggins-lab/SuperSegger] Not opening : Delete dust, bubbles and other bad regions (#1)

The warning is totally fine - it should not stop the program. Did it stop at that point? I would be happy to look into it if you send me 5-10 of the pictures you were using. I did fix a couple of things recently, could you please download the newest version of SuperSegger and try it again? Just to make sure this wasn't from an older version! Thank you!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

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mxardre commented 7 years ago

Solved thanks to stellastyl. Reopening of the xy1/seg/ in the window "Training new segmentation constant" by clicking on the file in the toolbar.