Question/ issue: Does mesmerise-core work with 3D movies?

[rajlakshmi-sawale]

Hi, does mesmerise-core work with 3D movies? I tried to run it with my xyzt data but the mcorr failed. Any help would be appreciated!
Thanks!

[ethanbb]

Hi @rajlakshmi-sawale, is it failing at the local correlations step? If so, #300 is meant to address this, but it hasn't been merged yet.

[ethanbb]

OK I just merged that PR; can you try again after installing from the master branch? You will also need caiman version 1.11.2 or later.

[rajlakshmi-sawale]

Hi @ethanbb, Thanks for the quick reply!
I'm not sure where it is failing.. I have attached what I see.. Sorry, I might not be running it in the right way in the first place as I am very new to this.

[ethanbb]

Yup, that looks normal, it ran into an error while running but it didn't tell you exactly what it is.

What does it show if you run print(df.iloc[-1, :].outputs['traceback'])?

[rajlakshmi-sawale]

This:

[rajlakshmi-sawale]

To run it on 3D data, do we have to specify any additional parameters?
The only thing I changed so far in the provided notebook for 2D data was in this section:

# We will start with one version of parameters mcorr_params1 =\ { 'main': # this key is necessary for specifying that these are the "main" params for the algorithm { 'max_shifts': [5, 5, 2], 'strides': [24, 24, 6], 'overlaps': [12, 12, 2], 'max_deviation_rigid': 3, 'border_nan': 'copy', 'pw_rigid': True, 'gSig_filt': None }, }

[ethanbb]

Oh ok you might need to use a different index than -1. If you just print the df you should be able to see which row corresponds to the failed run ("outputs" should be a dict with "success": False) and then you can use that index.

[rajlakshmi-sawale]

[kushalkolar]

The traceback in the output doesn't have to be accessed manually, you can call get_output() and it will print the traceback nicely:

df.iloc[i].mcorr.get_output()

[ethanbb]

Ah, I think you also have to set is3D to true in your params['main'].

[rajlakshmi-sawale]

Hi, I re-installed it and got this error:

[kushalkolar]

Reload the dataframe from disk after running an item

[rajlakshmi-sawale]

[kushalkolar]

The message says you're out of RAM. What are the dimensions of the movie? How many pixels do you have per neuron/ROI? What's your temporal sampling rate? Can you post a mean projectiom of some of the planes.