Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • Jan 10 15:20
    Blastorios closed #77
  • Jan 10 15:20
    Blastorios commented #77
  • Jan 10 15:19
    Blastorios opened #79
  • Dec 24 2021 23:02
    kushalkolar commented #77
  • Dec 24 2021 23:01

    kushalkolar on new-readme

    (compare)

  • Dec 16 2021 02:31
    kushalkolar closed #78
  • Dec 16 2021 02:31

    kushalkolar on master

    updated tifffile.imsave to save… Merge pull request #78 from Eri… (compare)

  • Dec 16 2021 02:31
    kushalkolar commented #78
  • Dec 15 2021 15:30
    EricThomson opened #78
  • Nov 15 2021 19:08
    Blastorios synchronize #77
  • Nov 15 2021 18:56
    Blastorios synchronize #77
  • Nov 15 2021 17:59
    Blastorios synchronize #77
  • Nov 15 2021 15:53
    TundeSzungyi closed #75
  • Nov 15 2021 15:53
    TundeSzungyi commented #75
  • Nov 15 2021 12:10
    Blastorios opened #77
  • Nov 14 2021 21:29
    kushalkolar commented #76
  • Nov 14 2021 21:08
    kushalkolar commented #75
  • Nov 14 2021 14:25
    TundeSzungyi edited #75
  • Nov 14 2021 14:24
    TundeSzungyi edited #75
  • Nov 14 2021 14:23
    TundeSzungyi edited #76
Michelle Jin
@mjin1812
Thanks for the fast response! I will definitely check out the notebook. For reference here is a link to a screenshot showing the difference in frame rates https://imgur.com/a/HMLush2
perhaps I just entered the metadata wrong. I followed the instructions only on entering it manually
Kushal Kolar
@kushalkolar
what method are you using to create the cnmfe batch items?
Michelle Jin
@mjin1812
I used the batch manager gui
Or mean the cnmfe gui to add to the batch manager
For reference, I'm using mesmerize through the VM installation
Kushal Kolar
@kushalkolar
@mjin1812 just took a look, the GUI sets the framerate at the component evaluation stage which appears to be when CNMFE uses the framerate, though I don't know why this doesn't show up in the cnmf_data_dict
Michelle Jin
@mjin1812
Thanks for your help! Does the gui automatically set the frame rate using the metadata dictionary? If so, then maybe I’ll just go with that value
Kushal Kolar
@kushalkolar
@mjin1812 The GUI does set the fps but only at the evaluate_components() step which might be why it's not showing up in the cnmf_data_dict. Anyways I'll put in a fix so that it's set at the very beginning and then it should show up in cnmf_data_dict
Michelle Jin
@mjin1812
Hi Kushal! Can I clarify whether 'cnmf_idx' in the 'ROI_states' series of a transmission object dataframe is corresponding to the roi indices in a traditional cnmf estimates object?
Kushal Kolar
@kushalkolar
yes, it's the originating cnmf.estimates.idxvalue for that ROI
Michelle Jin
@mjin1812
Thank you!
Serapio M. Baca
@smbaca
Does anyone have any experience with using mesmerize on a cluster? We have to request number of cores, RAM, GPU or no but then we have a 10TB scratch space and can use a Desktop environment running CentOS below to access mesmerize. So far, I have been able to run the motion correction but then the cnmf-e fails with not being able to find a file.
I am using Eric Thomson's instructions on the windows installation so I know that it is not a problem with the tiff movie.
Kushal Kolar
@kushalkolar
@smbaca this will probably be easiest to solve if you post an issue with all the details :)
You will probably have to set a workdir and it will need to be mounted at the same location on the compute nodes and the submission machine, but if you post an issue I can help with the details
Serapio M. Baca
@smbaca
Ok, posted the error message in the other location. Program seems to want to create a file in /var/www/ood... and that is not an installed directory.
Michelle Jin
@mjin1812
Hi Kushal! I follow instructions online to export and open up a transmission object externally in python. I detected what I think may be an indexing issue in the transmission dataframe. The "_DFOF" traces and "_RAW_CURVE" traces aren't lining up for me. I plotted the calculated dfof and raw curves for three consecutive rois using the code below where t is the transmission object and n is my roi index:
ax.plot( t.df["_DFOF"].iloc[n]); ax.plot( t.df["_RAW_CURVE"].iloc[n]);
Here is the plot for the three consecutive rois: https://imgur.com/a/nHUJ5ly Orange = "_RAW_CURVE" blue = "_DFOF"
It looks like the DFOF traces in blue matches with the orange trace of the previous roi
Kushal Kolar
@kushalkolar
@mjin1812 I'm away until next Wednesday so I'll get back to you then.
Eric Thomson
@EricThomson
Congratulations on some great software and a great paper @kushalkolar !!!
Kushal Kolar
@kushalkolar
@mjin1812 Did manually remove ROIs in the Mesmerize ROI manager or from the cnmf.estimate object?
2 replies
Irene Ayuso
@AyusoAa
Hi Kushal, congratulations for the paper! I was wondering if it is possible that the MC output file get the name of the orinial file instead of a collection of letters and numbers. When trying a bunch of parameters for CNMF-E, It is very slow to have to check the match between the original filename and the mc filename everytime. Coud you give some tips on how to change that in the code?
Kushal Kolar
@kushalkolar
@mjin1812 I'm not sure what was causing the issue then in that one case but it seems like it only occurred once so I'm not too concerned.
@AyusoAa I'm not sure what you're trying to do. If you use the batch manager interface you don't need to know the uuids for each item to iterate over parameter variants.
WhereWolf72
@WhereWolf72
@kushalkolar Congrats on the paper! I'm having some trouble getting the metadata (specifically the frames per second) to be loaded properly to run CaImAn's CNMF-E. I am almost certain the problem is on my end, but I can't seem to troubleshoot it. The files were acquired via Nikon Elements, so they were originally .nd2 files. I manually added "fps = __" into the metadata for each as our Elements only uses frame acquisition rate (seconds per frame), and then converted to TIFFs via Elements. Finally, I have deinterleaved the two-channel images into just the channel for the calcium imaging using FIJI. In the end, none of the metadata loaders will recognize the image file as containing the fps metadata. Any help or advice would be greatly appreciated, thank you!
Kushal Kolar
@kushalkolar
@WhereWolf72 you can create a json file with the same name as the tiff file that has the structure of the "json_minimal" described here http://docs.mesmerizelab.org/en/master/user_guides/viewer/modules/tiff_file.html#module-tifffile-metadata
2 replies
danielmichaelvirga
@danielmichaelvirga
Hi, is there any way to import an .h5 file which contains all of the Ca2+ imaging data rather than use a .tiff?
Kushal Kolar
@kushalkolar