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nel-lab / mesmerize-core

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
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Computer crashes with cnmf.run_detrend_dfof #276

Closed restrepd closed 6 months ago

restrepd commented 6 months ago

I am trying to get dFF and my computer crashes

I run mcorr_cnmf.ipynb. The code below calls

df.iloc[index].cnmf.run_detrend_dfof(quantileMin=8, frames_window=250, flag_auto=True, use_fast=True, use_residuals=True, detrend_only=False)

The computer becomes busy and gives this message several times: "WARNING:root:Percentile computation failed. Duplicating and trying again."

It then crashes and re-starts.

Our computer runs Ubuntu:

No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy

Jupyter lab python 3.11.7

I also need information on how to read your hdf5 file in matlab.

Thanks!

Diego Restrepo

kushalkolar commented 6 months ago

This is a caiman level issue, I suspect it's related to this: https://github.com/flatironinstitute/CaImAn/issues/1274

I'm going to close the issue here and refer you to that issue on caiman.

restrepd commented 6 months ago

Thanks!

Diego

Diego Restrepo, PhD Professor of Cell and Developmental Biology http://www.restrepolab.org/ University of Colorado Anschutz Medical Campus Department of Cell and Developmental Biology MS 8108 Bldg RC1 South, Room L18-11119 12801 E 17th Ave Aurora, CO 80045

Tel: 303-724-3405 Fax:303-724-3420

From: Kushal Kolar @.> Date: Tuesday, February 13, 2024 at 8:05 PM To: nel-lab/mesmerize-core @.> Cc: Restrepo, Diego @.>, Author @.> Subject: Re: [nel-lab/mesmerize-core] Computer crashes with cnmf.run_detrend_dfof (Issue #276) [External Email - Use Caution]

This is a caiman level issue, I suspect it's related to this: flatironinstitute/CaImAn#1274https://github.com/flatironinstitute/CaImAn/issues/1274

I'm going to close the issue here and refer you to that issue on caiman.

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