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Bilalgp
@Bilalgp
Apologies for the late response. Thank you for the prompt reply. Just to clarify, for the Caiman functions, I should a previous generated Ain variable into the Ain entry in a new analysis? Should the previous Ain variable be loaded from the cnmf class?
Kushal Kolar
@kushalkolar

@Bilalgp
For CNMF:
If you have an Ain array from a cnmf object, just save it using numpy.save(), and place it in the batch path with the filename: <uuid>.ain and check the "Seed components from mask" checkbox in the CNMF params GUI.

For CNMFE:
Currently you can only use ROIs from a previous CNMFE item that already exists in the batch manager. Just enter the UUID of the previous item in the Ain line entry.

14 replies
Bilalgp
@Bilalgp
image.png
kir0ul
@kir0ul:matrix.org
[m]
Hi there, quick question: can I export ROIs and calcium traces with Mesmerize? And if yes in which format(s)?
Kushal Kolar
@kushalkolar
@kir0ul:matrix.org Do you want to save it to a mesmerize project or do you just want to save the work environment in the viewer?
9 replies
kir0ul
@kir0ul:matrix.org
[m]
I'll have a look at that, thanks @kushalkolar!
Kushal Kolar
@kushalkolar
We have an importable VM that you can use to get up & running with Mesmerize within minutes if you don't want to setup virtual/conda envs etc. http://docs.mesmerizelab.org/en/master/user_guides/installation.html#all-platforms
1 reply
Eric Thomson
@EricThomson
In the ROI manager is 'curve data' the rows of C from the caiman estimates class?
Kushal Kolar
@kushalkolar
@EricThomson Yes, and spikes is from S
Eric Thomson
@EricThomson
Thanks. If I pull data from a cnmfe result using the flowchart will it automatically default to C? I'm having a flowchart where it seems to not be finding data, a case where I didn't calculate dff. But not sure if that's the issue or not. :)
But in my initial test project it worked when I did calculate dff.
Kushal Kolar
@kushalkolar
_RAW_CURVE will be C
Eric Thomson
@EricThomson
Ah cool thanks let me give it a go :)
Kushal Kolar
@kushalkolar
If dF/Fo isn't available it just throws a warning but you can work with the raw curve or spikes (i.e. estimates.C or S if from CNMF)
Eric Thomson
@EricThomson
Would I click add node->data-> ?
Kushal Kolar
@kushalkolar
You can choose the data column you want to plot or work with in most flowchart nodes
Yes, LoadProjDF
Eric Thomson
@EricThomson
Ok thanks that's what I am doing. Let me look at the docs here I've just been doing the vids.
Eric Thomson
@EricThomson
Maybe it is an idiosyncratic problem with this one dataset as I'm getting 463: UserWarning: ROI does not contain the following data attribute: dfof_data
And the flowcharts are just not happy with anything I'm doing.
Kushal Kolar
@kushalkolar
that's just a userwarning that shows up whenever dfof data are missing
What does your flowchart look like?
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 :)