Fixes to Perens and Kim mouse atlases

[viktorpm]

Description

This PR fixes IndexError: tuple index out of range of perens_lsfm_mouse.py (see: #249) and the orientation and scaling issue of perens_lsfm_moue and kim_mouse atlases mentioned in #265

What is this PR

• [x] Bug fix
• [ ] Addition of a new feature
• [ ] Other

What does this PR do?

fixes #265

References

265

How has this PR been tested?

tested on HPC and locally

Is this a breaking change?

no

Does this PR require an update to the documentation?

Yes, when new versions of the atlases are published

Checklist:

• [x] The code has been tested locally
• [ ] Tests have been added to cover all new functionality (unit & integration)
• [ ] The documentation has been updated to reflect any changes
• [ ] The code has been formatted with pre-commit

[viktorpm]

Errors to be solved:

Script - error number	Error	Note	Solved
admba_3d_dev_mouse.py - 2	gets stuck at region 112892417 of admba_3d_p28_mouse	Creating mesh for region 112892417 No labels found for r10LimCG (112892417)	no
admba_3d_dev_mouse.py - 3	doesn't skip already generated atlases	FileExistsError: [Errno 17] File exists:	no
humanatlas.py - 1	FileNotFoundError: No such file or no access: 'D:\Dropbox (UCL -SWC...'	hardcoded paths in the code	no, needs separate PR
mpin_zfish.py - 2	SSLError: HTTPSConnectionPool(...)	-	no
perens_lsfm_mouse.py - 1	IndexError: tuple index out of range	yes

perens IndexError: tuple index out of range error is fixed

[viktorpm]

perens orientation issue is fixed

[viktorpm]

Atlas generation on HPC:

#!/bin/bash

#SBATCH -p cpu # partition (queue)
#SBATCH -N 1   # number of nodes
#SBATCH --mem 160G # memory pool for all cores
#SBATCH -n 10
#SBATCH -t 0-8:0 # time (D-HH:MM)
#SBATCH -o atlas_regeneration.out
#SBATCH -e atlas_regeneration.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=v.plattner@ucl.ac.uk

# Load mamba module
module load mamba

# Initialize mamba
mamba init

# Create environment
#mamba create -n bg-atlasapi python=3.11

# Activate environment
mamba activate bg-atlasapi

cd _projects

# Clone repository
git clone https://github.com/brainglobe/brainglobe-atlasapi.git

# Navigate to repository directory
cd brainglobe-atlasapi/

# Checkout specific branch
git checkout issue_265

# Install required packages
pip install -e ".[allenmouse, dev]"
# pip install .
# pip install .[allenmouse,dev]
# pip install brainglobe-atlasapi
# pip install brainglobe-atlasapi[allenmouse,dev]
pip install scikit-image
pip install imio
pip install brainio

# Navigate to specific directory
cd brainglobe_atlasapi/atlas_generation/atlas_scripts

# Define resolutions
resolutions=(100 50 25 10)

# Loop over resolutions and run the script for each
for resolution in "${resolutions[@]}"; do
    python kim_mouse.py --resolution=$resolution
done

[viktorpm]

New atlases were generated using the updated script. Once they pass the validation functions, they can be published.

kim_mouse_25um:

[viktorpm]

Passed the validation functions (without the additional_references functions, see #275): validation_results.json

• kim_mouse_25um
• kim_mouse_50um
• kim_mouse_100um
• perens_lsfm_mouse_20um

kim_mouse_10um is still being regenerated

[viktorpm]

kim_mouse_10um passed the validation functions

[adamltyson]

Does this also close https://github.com/brainglobe/brainglobe-atlasapi/issues/247?

[viktorpm]

Yes, it does