https://github.com/biop/quick-start-czi-reader
A bio-formats image reader for CZI that starts faster
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary
Repository
A bio-formats image reader for CZI that starts faster
Basic Info
- Host: GitHub
- Owner: BIOP
- Language: Java
- Default Branch: main
- Size: 23.2 MB
Statistics
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 7
- Releases: 0
Metadata Files
README.md
STATUS
This project can't move forward. The initial ambition was to replace the inefficiencies of the original Bio-Formats CZI reader. Unfortunately, the OME team maintains exclusive access to CZI files that only they can test. Coupled with the burden of integrating a major rewrite, the PR I had hoped would be merged will never be merged (https://github.com/ome/bioformats/pull/4092). So instead of being part of the solution and making a contribution to the open-source community, this extra reader adds—yet again—more complexity to the problem.
That's a disgrace.
Zeiss Quick start CZI Reader
This reader can be used starting from Bio-Formats version 7.1.0 and above.
Quick start Bio-Formats CZI reader
A revamped version of the original ZeissCZIReader which parses faster the metadata. This is critical to open multi-TB files in Fiji in a reasonable amount of time.
This new reader is tested against a list of publicly available CZI files.
For more information see: - the original issue - a draft PR on Bio-Formats - go to the compare folder of this repository to see how this readers differs from the bio-formats reader for a set of publicly available czi files
To use this reader instead of the original one, you will need to activate the Fiji update site Zeiss Quick Start Reader and by enabling the Zeiss(CZI) Quick Start reader in the Bio-Formats plugins configuration.
Special thanks to Zeiss for opening its file format and allowing open source software to improve!
Owner
- Name: BioImaging And Optics Platform (BIOP)
- Login: BIOP
- Kind: organization
- Location: Lausanne, Switzerland
- Website: https://biop.epfl.ch
- Repositories: 84
- Profile: https://github.com/BIOP
All the code that is publicly available/published by the BioImaging And Optics Platform (BIOP)
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Issue comment event: 2
- Push event: 4
- Create event: 1
Last Year
- Issues event: 1
- Watch event: 1
- Issue comment event: 2
- Push event: 4
- Create event: 1
Dependencies
- actions/checkout v2 composite
- actions/setup-java v3 composite
- ome:formats-api
- ome:formats-bsd
- net.imagej:imagej test
- net.imagej:imagej-legacy test
- ome:bio-formats_plugins test
- ome:formats-gpl test
- org.apache.commons:commons-lang3 test