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
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
Is there a way to show rejected components in the ROI manager?
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 use the --upgrade flag https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/?highlight=--upgrade#upgrading-packages
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.
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
@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
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
Hi there, quick question: can I export ROIs and calcium traces with Mesmerize? And if yes in which format(s)?
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
But in my initial test project it worked when I did calculate dff.
Yes, LoadProjDF
And the flowcharts are just not happy with anything I'm doing.
What does your flowchart look like?
But I will post screenshot
