allen2quicknii

Command line script for downloading series from the Allen data portal into QuickNII-compatible package.

This script has been tested with in-situ hybridization datasets and connectivity (block-face) datasets. It creates images and ancillary files (xml) compatible with QuickNII mouse. It only works with ABA template at 25 micrometers isotropic voxel.

Dependencies

requests : part of (Ana)conda, or can be installed with pip install requests

Usage

In conda

python allen2quicknii.py <series identifier>
python allen2quicknii.py --get-orig <series identifier>
python allen2quicknii.py --target-dir /data/AMBA/datsets/ <series identifier>

In iPython

run allen2quicknii.py <series identifier>
run allen2quicknii.py --get-orig <series identifier>
run allen2quicknii.py --target-dir /data/AMBA/datsets/ <series identifier>

Arguments

--get-orig if added, the original size images are downloaded. This mights take a lot of time (~5 minutes per file) "This might take a lot of time")

--target-dir TARGET_DIR the images and associated files are saved in TARGET_DIR folder

Note: full resolution images are provided in JPEG format, putting them into Navigator may involve additional hurdles.

Details description

• creates a folder for the series
• indicates when encountering unknown reference space. AMBA is #9 (tested, working so far), and #10 may work too (not tested).
• creates a complete QuickNII series, with downscaled images and accompanying ".xml" file, using registration data from Allen portal