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Oleg Tolstenkov
@olegtolstenkov_gitlab
Hello Kushal. I have a problem opening my project. /share/data/long-term/1/Oleg/For_analysis/Embrio_set2/Tailbud/Projects/Set_1 Could you help please? Thanks.
Kushal Kolar
@kushalkolar
@olegtolstenkov_gitlab I'm currently away so I can check this on Monday.
Kushal Kolar
@kushalkolar
@olegtolstenkov_gitlab Fixed. Your root dataframe file was truncated, you probably ran out of disc space while the file was saving. So I restored the latest root dataframe backup present in the dataframes directory, it should have everything except the most recently added project sample. I'd suggest you move your data to another drive. Please perform this move via master and not via node.
Also your project config file was blank so I restored it based on the project's root dataframe. You can modify it as you wish from within Mesmerize.
Tom Vajtay
@tvajtay
So for my scenario I have a series of videos that I would like to batch process (NoRMcore -> CNMF -> crosscor components), what would be the best way to do that?
Using Mesmerize
What I understand so far is that I would after defining a project would open the viewer to start select files but I'm not getting something
Kushal Kolar
@kushalkolar
  1. Open the image sequence using the tifffile module or console. You can either create json files in the specified format or set meta data manually. Framerate is the main piece of meta data that's required.
  2. Use the Caiman Motion Correction module to add the current Viewer Work Environment (i.e. the image sequence with its meta data) as a "batch item". You can create multiple such items with different variants of parameters. You can use the module either via the GUI or the console.
  3. Use the outputs from the Caiman Motion COrrection batch items to create CNMF batch items. You again have the option of using a script to add them automatically or manually with the GUI.
  4. Create a project with a configuration the pertains to your biological questions & add the CNMF outputs to the project. You can then use the flowchart for cross correlation analysis and other things.
You do not necessarily need to create a project until you have CNMF outputs.
Tom Vajtay
@tvajtay
So it is also possible to just use a folder of CNMF output HDF5's as well?
Kushal Kolar
@kushalkolar
There's no built in way to import the caiman CNMF output directly but it should be technically possible. The CNMF output will need to be used to create a ViewerWorkEnvironment object (that contains a ManagerCNMF object which has a few more things than cnmA, cnmB, cnmC etc. from the CNMF outputs.)
Tom Vajtay
@tvajtay
I can't seem to be able to manually edit metadata in GUI, can I add multiple videos to batch simultaneously?
Kushal Kolar
@kushalkolar
Yea you can only edit metadata through the console. Yes you can add many videos to a batch using a script
there are some examples for motion corr, cnmf and cnmfe
Tom Vajtay
@tvajtay
@kushalkolar have you looked into the Neurodata without borders format? (HDF5 re-skin with standardized attributes)
Kushal Kolar
@kushalkolar
I just took a look, I could add a viewer module to open image sequences contained in them. How do you use it?
As in, do you use it for anything other than storing image sequences?
Tom Vajtay
@tvajtay
I haven't started using it yet, I was trying to think about how to incorporate it. I know CaImAn can save the output in the NWB format but I'm just investigating at the moment.
I've also only recently discovered the 4GB limit for 32bit Tiff files and am also trying to resolve storing bigger movies
Kushal Kolar
@kushalkolar
I just downloaded a dataset and I'm trying to figure out how to open it. I could incorporate at least that for now, and it could technically be possible to export a mesmerize work environment to nwb format; but Mesmerize has a lot more attributes for the data.
You can create larger tiffs! How are you creating tiffs?
We regulargly have ~12GB tiffs
Tom Vajtay
@tvajtay
Yes the BigTiff format, 64bit
Kushal Kolar
@kushalkolar
by the way Zarr looks like an interesting project that I came across recently, haven't tried it https://zarr.readthedocs.io/en/stable/