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Kushal Kolar
@kushalkolar
@kevinpan0127 This seems like a Windows multiprocessing issue, can you post and issue with the entire traceback
VivoNeuro
@VivoNeuro
Hi,
I am just installing (win10) mesmerize following the steps on Read the Docs. I did all the 10 steps except 6 (pip install bottleneck==1.2.1, here it sent me a message: Microsoft Visual C++ 14.0 or greater is required; but these 5-6 steps are optional). When I tried to launch mesmerize it sent me: ModuleNotFoundError: No module named 'tslearn.cycc'. Could you help me? Thank you
16 replies
Bilalgp
@Bilalgp
I am having trouble displaying the dF/F in the ROI Manager. Do you know how I can troubleshoot?
image.png
Kushal Kolar
@kushalkolar
you must compute them first, it's one of the caiman modules
Bilalgp
@Bilalgp
Thanks! @kushalkolar !
Is there a way to show rejected components in the ROI manager?
Kushal Kolar
@kushalkolar
@Bilalgp there currently isn't but if you make a feature request on the issue tracker I'll look into it for a future version of mesmerize :)
Bilalgp
@Bilalgp
Great thanks.
I also just noticed for a dataset, the ROIs for the caiman HDF5 file aren't correctly matching with that in Mesmerize (traces are correctly numbered but being for the wrong ROI on the map). I am not sure if this problem is because of my Caiman pipeline so I'll investigate but I thought I should let you know.
1 reply
kevinpan0127
@kevinpan0127
@kushalkolar I was wondering how should I update v0.5.0? thank you very much!
sneezeman
@sneezeman
Hello there!
I'm trying to follow the youtube tutorials, but so far I can't reproduce even the first steps: stimulus import/export and batch motion correction
I'm on Ubuntu 18.04.3, used pip to install mezmerise.
So, problems: when I click on export/import buttons in Stimulus Mapping window, nothing happens, and no error is shown in the console. Otherwise, the Stimulus Mapping works.
With batch processing I can add the tasks, but when I click Start, it looks like it starts to work, but no output appears in the additional console. Again, no errors in the main console.
@sneezeman I've also checked that caiman works in this environment, and it does work
Kushal Kolar
@kushalkolar
@sneezeman the import & export buttons on the stimmapping module are not functional, you can import stimmaps from sources such as csv/xls files using the script editor or enter a stimmap manually.
@sneezeman for the batch manager, make sure your system configuration is setup properly. See the steps at the end of the installation for details.
Bilalgp
@Bilalgp
Hi. I am interested in tracking a specific ROI generated from Caiman on more videos besides the boundaries used in generating that ROI. Is there any way to do this in Mesmerize?
Kushal Kolar
@kushalkolar
@Bilalgp Do you mean that you want to use the ROIs from one video's CNMF(E) output to see the ROIs for performing CNMF(E) on other videos?
Kushal Kolar
@kushalkolar
@Bilalgp
You can seed a CNMF(E) batch item by either:
  1. Passing the UUID of a prior batch item in the same batch to the Ain entry in the CNMF(E) module GUI.
  2. Saving a sparse mask (that can be loaded through numpy.load() in the batch dir with the filename: <item_uuid>.ain
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).