Manual labelling ROIs - data saving

[dkushinsky]

Hi,

Thanks so much for the added feature of manually labeling ROIs! Unfortunately, the extracted traces from the manually labeled ROIs are not being saved, as it seems that the 'save and exit' button is not available (as can be seen in the screenshot below). Is there something I am missing? I am currently using the github version of the code.

Thanks!

[LurLab-UCI]

Hi,

First of all, huge shout out to the developers; suie2p is simply wonderful! I have bumped into the same issue as the OP though: "save and quit" button in manual labeling not functional (see image). It seems to be overlapping with the "mean image button". My original thoughts were that I messed up the install, but then I saw that it's not an issue unique to me.

test system: i5-8350U CPU 16B RAM 256 GB SSD GeForce MX150 Windows 64-bit (Home)

anconda 64-bit python 3.7.5 conda 4.8 all packages in the suite2p environment updated to latest version (as of Dec. 18, 2019). install: went quite smoothly as described in https://github.com/MouseLand/suite2p except: some packages defined in the environment.yml did not install automatically, had to be conda or pip installed manually.

test data: tested on 3 different single channel 2P imaging data sets, 256x256 or 512x512 resolution, 30 or 15 FS, as well as on a couple of 2-channel sets. Test images were short tiff stacks recorded in ScanImage on a Sutter MOM, 1000, 1500 and 2000 frames.

Thank you for your help!

[mathildelpx]

Hi!

To follow on this issue I also encounter a problem regarding this new function. I have access to the window 'extract ROI activity' but don't have the 'save and quit' button.

OS is Xenial, with Linus Mint. I installed the git hub version within conda env created with your .yml file, with no error message. anaconda 64-bit conda 4.8 python 3.7.4 Everything is up to date.

Hoping this helps to understand the issue ! Thanks!

[carsen-stringer]

sorry about this, please clone the latest github repository

[carsen-stringer]

please comment if you still have issues, I will close this for now

[tomMEM]

Hello, I also tested the new version (pip install suite2p --upgrade, 30.12.2019) and I could not find a way to save the new transients. In one of the previous version I saw a button (load to GUI). All the best for the new year. Thomas

A second item: It seems that strings of a networks path are going to be mixed up with (\ to / ) if they are unreasonable long, so that files can not be loaded or saved.

[mathildelpx]

Hi, I think the correction of this feature was made on the github version only, for me it works perfectly with it now.

On Wed 1 Jan 2020 at 8:46 AM, Thomas notifications@github.com wrote:

Hello, I also tested the new version (pip install suite2p --upgrade, 30.12.2019) and I could not find a way to save the new transients. In one of the previous version I saw a button (load to GUI). All the best for the new year. Thomas

A second item: It seems that strings of a networks path are going to be mixed up with (\ to / ) if they are unreasonable long, so that files can not be loaded or saved.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MouseLand/suite2p/issues/265?email_source=notifications&email_token=AMB3FH7WFF5RXUJ3XVUD6ODQ3RC47A5CNFSM4J27HLP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEH474ZQ#issuecomment-570031718, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMB3FH6F23F7NKFSNI5DRSTQ3RC47ANCNFSM4J27HLPQ .

-- Mathilde Lapoix PhD student Institut du Cerveau et de la Moelle - ICM MD student Ecole de l'INSERM Liliane Bettencourt

[LurLab-UCI]

Github version worked for me as well.
Thanks !

[tomMEM]

Hello, using last github version and new environment.yml based installation after deleting old environment works nicely (sparse_mode: 1).
Is it possible to load same ROIs for the analysis of subsequent time-lapse sessions? Best.