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Eric Thomson
@EricThomson
But the ROI manager is working fine. ¯\_(ツ)_/¯
Kushal Kolar
@kushalkolar
yup it's just a warning, not an exception
Eric Thomson
@EricThomson
Data to z score to heatmap
Kushal Kolar
@kushalkolar
If you can paste a screenshot I can see if something is weird
Eric Thomson
@EricThomson
First giveaway z score data column not giving any options
But I will post screenshot
image.png
Kushal Kolar
@kushalkolar
There's nothing coming out of the Load_Proj_DF node, if you click on it it'll show the message in the bottom panel
Eric Thomson
@EricThomson
That's embarrassing you are right. Columns must be same length as key (valueerror).
Kushal Kolar
@kushalkolar
strange, did you encounter issues while adding samples to the project?
Eric Thomson
@EricThomson
No everything is fine up through ROI manager. This is some strange data though (we have dendrites and I'm using some weird parameters for 1p data), but given that it looks very good.
Kushal Kolar
@kushalkolar
what does your project browser look like?
Eric Thomson
@EricThomson
It is empty.
Kushal Kolar
@kushalkolar
sorry if this is dumb question, but I'm assuming you went through this? http://docs.mesmerizelab.org/en/master/user_guides/viewer/add_to_project.html
Eric Thomson
@EricThomson
I'm sure I did something dumb
Kushal Kolar
@kushalkolar
After you have all your ROIs and annotations etc. in the viewer the way that you like it, you need to add the "Viewer work environment" to the "Project Dataset"
Eric Thomson
@EricThomson
I may have left out a step with this second project
ffs I'm sorry for wasting your time let me do this and then try
Kushal Kolar
@kushalkolar
No worries, Mesmerize is quite massive :)
Eric Thomson
@EricThomson
Crap now everything is showing up thanks a lot I was being an idiot.
I followed the video to the letter with first project and then tried to do from memory for this second one. Again, I'm really sorry about that.
Will be more careful next time!
Kushal Kolar
@kushalkolar
No worries, always happy to see new users!
Eric Thomson
@EricThomson
I appreciate it. As a new thing I've noticed: I think the images in the projection viewer generated from the pipeline the y axis is inverted compared to in the standard viewer.
Kushal Kolar
@kushalkolar
That might be true, I could take a look
Eric Thomson
@EricThomson
When I finish all this exploring I'm sure it would be something I could fix and make a PR. I'm presenting this tomorrow at lab meeting. :)
Kushal Kolar
@kushalkolar
I'd be happy to see a PR :) . I think you'd need to play around with this on line 27 https://github.com/kushalkolar/MESmerize/blob/master/mesmerize/viewer/image_menu/image_projections.py
And thanks, our goal is to make FAIR data principles more common in biology :)
Eric Thomson
@EricThomson
Sounds great!
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?