MESmerize/community

Kushal Kolar

@kushalkolar

Hi @kevinpan0127, replied to your issue on github

kevinpan0127

@kevinpan0127

Hi @kushalkolar, I am now trying to run the CNMF module and i am getting getting stuck with the following message:

RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

===== 2020.12.27 20:12:44 =====

Is there something that I am doing incorrectly? Thank you!

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?

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!

Kushal Kolar

@kushalkolar

@kevinpan0127 use the --upgrade flag https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/?highlight=--upgrade#upgrading-packages

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:

Passing the UUID of a prior batch item in the same batch to the Ain entry in the CNMF(E) module GUI.
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

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

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