Need help using Mesmerize

[maxrioux100]

First of all, im on ubuntu 20.04 LTS FRESH INSTALL only for this. I tried both installation method but I would prefer to make the github one work (since it has less limitations)

When I open mesmerize from the snap installation. I get [Errno 13] permission denied joblib will operate in serial mode. I tried to give all the right to /dev/shm but the error persist.

On the other hand. with thee github installation everything looks fine(except for some numpy warning when running python setup.py build_ext -i)

However I cant seem to make the motion correction work. The tif file load perfectly and the batch manager receive it but it always end up red or orange.

How can I solve this and complete it.

Thanks a lot

[kushalkolar]

Can you click on the batch item to display the output. Can you also give me a screenshot of the system config window. http://mesmerizelab.org/user_guides/general/misc.html#system-configuration

[maxrioux100]

[kushalkolar]

Did you install using the snap branch?

[maxrioux100]

yes as you said in the guide

Clone the mesmerize repo and enter it:

git clone https://github.com/kushalkolar/MESmerize.git cd MESmerize

Checkout the snap branch:

git checkout snap

[kushalkolar]

I think you need to add the following lines to your system config:

export PATH=<path to python environment for mesmerize> export PYTHONPATH=<path to MESmerize dir>

See the points about "Pre-run commands" here for more details: http://mesmerizelab.org/user_guides/general/misc.html#system-configuration

[maxrioux100]

But even with that, I get the same result

[kushalkolar]

Sorry about this, this seems to have been created by an update to the snap branch a few days ago. I just fixed it so if you run git pull in the MESmerize dir it should pull the fix and you should be able to run motion correction :)

[maxrioux100]

No problem, I test this out !

[maxrioux100]

I think this is working now. (I say think because the motion correction dont finish but I blame the computer I use because he dont have a really good precessor) I will try to install linux on a computer that I already tested caiman successfully on it. thank you for your fast response.