Published August 21, 2019
| Version 0.1
Software
Open
Perl script for batch processing of ACQUIFER Imaging Machine data via Fiji macros
Description
Batch generation of multilayer tiff files and z-projection for 1-N IM04 datasets.
The Perl script will parse all IM04 datasets within a user-specified directory and will generate a Fiji macro to process each unique entry (i.e. imaging coordinate ,or “Coordinate--Subposition--Loop—Colour”).
The Fiji macro will subsequently generate colour specific subfolders within each experimental folder.
For each “Coordinate--Subposition--Loop—Colour” entry, multilayer tiffs and z-projections are generated. CO6 (=bright field) data will be minimum z-projected, all other channels are maximum z-projected.
Tested on Windows OS with Strawberry Perl (http://strawberryperl.com/).
Please ignore the first version.
Files
Files
(4.1 kB)
| Name | Size | Download all |
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md5:9478a5cbc7a5b00c764d30badbc47a19
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4.1 kB | Download |
Additional details
References
- Pandey, Gunjan, et al. "A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model." International journal of molecular sciences 20.6 (2019): 1290.
- Westhoff, Jens H., et al. "Development of an automated imaging pipeline for the analysis of the zebrafish larval kidney." PLoS One 8.12 (2013): e82137.