Add new segments

[imihalce]

Hi I use now a lot Super Segger. But some long run experiments, not always perfect optically, need some manual curing. Now that the manual link correction work, ( that helped a lot !!) would it be possible (in the long run) to add one or two more features: -in the Edit segment a manual tool where we would be able to add an new (inexistent) segment

• in the same window would it be possible (once manually cured) to check a box telling the optimization algorithm to hold those segments and unchange their designation. And last but not least I would like to have the same check box in the link Editor (as if a later segment edition erase all the link connections)

thanks again Irina

[pawiggins]

Hi Irina:

That is an interesting idea that we had considered but it hasn't been a huge priority... I'll chat with people in the group and see if anyone wants to add this feature.

Our general strategy is usually just to ignore cells with problems in our analyses.

--PAW

[imihalce]

Hi and thank you for your answer. Yes for other experiment is exactly what we are doing, just ignoring the badly segmented cells. And that works perfectly. However for these experiments they are long run with not so many cells, but that have to be followed all along so is crucial to not loose them. We tried to get around, suppressing some frames who "depressingly" getting us bad segments, but I think that would be much more easy just add some manual segments. My comment went along also with another question: it seems that when now that a successive segment editing suppress sometime the previously manually corrected segments. Would it be possible to have a flag for each frame were we would say to Segger do not change the segments here, do your optimisation before and after but not on this frame.

thanks a lot Irina

[pawiggins]

Hey Irina:

You can now create segments in "Edit Segments."

--PAW

[imihalce]

Hi and thank you for addressing so fast the issue . I updated now the Segger and it appears that the last version has some mishaps. I just have restarted a segmentation went for a coffee and when back, Segger produced something like open 300 figures. Could you keep the same configuration as before, to overwrite a new segmentation figure on top of the previous one ? Also in the SuperSeggerViewerGui the input for link editing is missing (from the wiki screen shot of the Viewer too).

best Irina

[pawiggins]

Hmmm…

When do the figures open and what do they have in them?

On Jul 26, 2018, at 11:32 AM, imihalce notifications@github.com wrote:

Hi and thank you for addressing so fast the issue . I updated now the Segger and it appears that the last version has some mishaps. I just have restarted a segmentation went for a coffee and when back, Segger produced something like open 300 figures. Could you keep the same configuration as before, to overwrite a new segmentation figure on top of the previous one ? Also in the SuperSeggerViewerGui the input for link editing is missing (from the wiki screen shot of the Viewer too).

best Irina

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wiggins-lab/SuperSegger/issues/16#issuecomment-408192875, or mute the thread https://github.com/notifications/unsubscribe-auth/Amb9oesAPtt4TejMT7aPQ65J7HKxH4XVks5uKgtAgaJpZM4VJ6hT.

[imihalce]

Hi, These figures are generated after the initial segmentation (end of step 2) and are some chunks of image (I bet is all around the problematic segment) with the segments superimposed on the phase image.

[pawiggins]

On Jul 27, 2018, at 2:05 AM, imihalce notifications@github.com wrote:

Hi, These figures are generated after the initial segmentation (end of step 2) and are some chunks of image (I bet is all around the problematic segment) with the segments superimposed on the phase image.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wiggins-lab/SuperSegger/issues/16#issuecomment-408359445, or mute the thread https://github.com/notifications/unsubscribe-auth/Amb9oUdZTw486RCa1Qg0CQsbAXYKBgo7ks5uKtfkgaJpZM4VJ6hT.

Hi Irina:

I don’t think that is anything new (at least not the direct results of new changes). I have seen that happen and that runs as part of something that Stella wrote. I am happy to try to fix it, but I probably need a minimal dataset from you to track down the problems. Is there a series of two to three cropped frames that can reproduce this problem?

—PAW