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Eric Thomson
@EricThomson
This is somewhat related to a question above: is there a way to save the results of the cnmf (cnmf-e) analysis so that back in the caiman pipeline I could run load_CNMF() and it will load results from mesmerize once we have reached the ROI viewer stage? Is it as simple as Transmission.to_hdf5: does that contain the estimates object needed for caiman to load?
Kushal Kolar
@kushalkolar
@EricThomson All the CNMF data are stored in the pickle files associated to each sample in <project_dir>/images. If you open them you can access the CNMF data dict through p['roi_states']['cnmf_data_dict']
I think caiman has a function only for loading from hdf5, but I have a function right at the top of mesmerize/viewer/modules/caiman_dfof.pywhich is basically the same as the load_CNMF() from hdf5 but does it from dict. (not sure if there's a function now that loads it from dicts)
If you have transmission object open, you can find the relative path to the pickle file for the current series using: t.df['ImageInfoPath']
Eric Thomson
@EricThomson
Very nice I will check all this out!
30 replies
Kaii
@SylarGraysonn_twitter
Hi! Could you pls tell me what does the curve data mean exactly? Why it has negative value?
I mean the RAW CURVE
Kushal Kolar
@kushalkolar
@SylarGraysonn_twitter if you used CNMF(E) _RAW_CURVEcorresonds to cnmf.estimates.C. If you used Manual ROIs, it's the mean intesnsity of the region under the ROI.
CNMFE will often output negative values for esimates.C
@SylarGraysonn_twitter see these for more info:
flatironinstitute/CaImAn#783
flatironinstitute/CaImAn#738
flatironinstitute/CaImAn#834
(and probably others in their repo)
as shown in those, if you decide that you want the non-negativity constraint you can enter bas_nonneg=True in the Use CNMF kwargs box just as you would enter the kwarg in a script http://docs.mesmerizelab.org/en/master/user_guides/viewer/modules/cnmfe.html
Eric Thomson
@EricThomson

In the mesmerize environment in a Jupyter notebook, trying to start a cluster cm.cluster.setup_cluster() I get an error that there is already one running (even if this is the first command I try to run: Exception: A cluster is already runnning. Terminate with dview.terminate() if you want to restart.).

I assume mesmerize environment fires up threads by default or something? I wonder if I can just access these and feed as argument to dview in setup_cluster(), or can I access/terminate the mesmerize cluster within Jupyter?

Or just as likely there is another better option and I'm thinking about this wrong. :)
Kushal Kolar
@kushalkolar
@EricThomson I have to figure out where the existing cluster is coming from, you can pass ignore_preexisting=True to caiman.cluster.setup_cluster() to get a new one
Kushal Kolar
@kushalkolar
There's isn't a worker pool, there's a SyncManager which is started. The caiman function just checks if multiprocessing.active_children() > 0. The SyncManager might be a pyqtgraph thing
Kushal Kolar
@kushalkolar
So basically, there is no divew intsance that's already running, it's a SyncManager and caiman.cluster.setupcluster() just checks multiprocessing.active_children() which contains a SyncManager. Pass ignore_preexisting=True to setup_cluster.
Eric Thomson
@EricThomson
Ah ok thanks I didn't noticed that parameter before will give this a go!
Eric Thomson
@EricThomson
Yes that did the trick.
katherinekelly2012
@katherinekelly2012
Hi, I am trying to do max projections and the program is not allowing me to export the videos. They load fine, but the program does not respond in any manner when I press export video. What do you think the error would be?
Kushal Kolar
@kushalkolar
Which export button are you clicking
@katherinekelly2012 the one above the histogram of the viewer?
katherinekelly2012
@katherinekelly2012
@kushalkolar Yes that's the one in the max projection pop up
Kushal Kolar
@kushalkolar
Ah, you can't export a video from a max projection. But you can export a video from the movie/image sequence shown in the viewer
I think you might need ffmpeg to be installed for the export.
katherinekelly2012
@katherinekelly2012
Yes, that is correct. I just installed ffmpeg into my mesmerize environment and I still can't seem to export the max projection.
Kushal Kolar
@kushalkolar
Yea, you can't make a movie from the max projection
But you can export the movie itself
@katherinekelly2012 click the same button but not in the max projection and you should be able to export
Kushal Kolar
@kushalkolar
image.png
you will get an export window like this
katherinekelly2012
@katherinekelly2012
Ok do you know why I would be getting this error: AssertionError: Unknown encoder extension? I've installed ffmpeg and x264. I previously thought it was functioning because I got the popup but when I go further it throws the previously mentioned error.
Kushal Kolar
@kushalkolar
@katherinekelly2012 I need the entire traceback
And what OS are you on etc.
BTW the issue tracker on GitHub is better for these types of things :)
katherinekelly2012
@katherinekelly2012
Ok thanks I can post there
Pradeep Rajasekhar
@pr4deepr
Hi @kushalkolar
If I import ROIs from ImageJ, instead of CNMF how will it affect the downstream analysis?
Cheers
Pradeep
i.e, can I still do peak analysis, k-shape etc?
Kushal Kolar
@kushalkolar
there's no difference, everything gets packaged into a project sample regardless of the signal extraction method
Pradeep Rajasekhar
@pr4deepr
Thanks @kushalkolar
Also, is there a spatiotemporal analysis component as well? Perhaps am missing something obvious.
Kushal Kolar
@kushalkolar
what do you mean?
Pradeep Rajasekhar
@pr4deepr
i.e., using coordinates or locations of the cells and their peak features to figure out changes in intercellular communication?
Kushal Kolar
@kushalkolar
You can add any number of labels you want to ROIs, which then get stored as categorical variables and you could see if peak features or the kshape clusters that data fall into are different based on those categoricla variables
Pradeep Rajasekhar
@pr4deepr
Maybe its the terminology I use. I should rephrase it to I am looking at correlations in activity between cells, so it still applies?
Kushal Kolar
@kushalkolar
correlation in activity is a different thing
Pradeep Rajasekhar
@pr4deepr
ahh
Pradeep Rajasekhar
@pr4deepr
So with the correlation we are using the temporal component, right?
Is it possible to add the spatial component to it as well?
Kushal Kolar
@kushalkolar
you mean ROI tags?
If you tag ROIs and then use the cross correlation GUI you can see the corresponding ROI tags in the plot http://docs.mesmerizelab.org/en/master/_images/cross_cor.gif
Eric Thomson
@EricThomson
I have many users that now want to use mesmerize, and we are wondering what the kind of minimal requirements are? I assume similar to caiman. I know caiman doesn't require NVidia GPU but does benefit from high RAM, high core count, good CPU, etc.. Is there a kind of "minimum suggested build" for mesmerize? There are people with gov't issued laptops that are not amazing. In terms of RAM it seems 64 is good can we get away with 32?
Eric Thomson
@EricThomson
(We are doing cnmf-e so don't use cnn based component exclusion so no need for gpu)