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May 15 18:11

JCKMes commented #99
May 15 17:43

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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

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)

Kushal Kolar

@kushalkolar

@EricThomson Yup in general the same requirements as Caiman if you're using those modules.

CNMFE is more resource intensive than CNMF. If your imaging resolution is ~512x512 and your movies are shorter than 10 mins you might be able to get away with 32GB or less. For longer movies I think it's recommended to use CNMFE online anyways. Faster RAM and quad channel RAM also seems to help for both CNMFE and motion correction (quad channel is usually only availalbe on Xeon and Threadripper I think).

For certain downstream things like computing Earth Mover's Distances like in our papers, very high thread count (64+) is necessary for large datasets (thousands of traces) and the computation will take days. Similar for kshape clustering.

Eric Thomson

@EricThomson

Thanks that's really helpful I will take this into consideration

Eric Thomson

@EricThomson

To run caiman motion correction in mesmerize without the piecewise motion correction, should it be enough to check the Use motion correction kwargs box and manually add in pw_rigid=False, and then just set the rigid correction params I want (and ignore the Elastic correction params)?

Kushal Kolar

@kushalkolar

Nope, I haven't added the option to perform just the rigid correction, is there a usecase where non-rigid doesn't work?

Eric Thomson

@EricThomson

There are cases where rigid is sufficient. Since it is a lot faster it is preferable in those cases (e.g., we have animals under anesthesia where there is not much movement, and rigid works well).

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