https://github.com/janeliascicomp/n5-tools-dask
Dask-based utilities to process N5 images
https://github.com/janeliascicomp/n5-tools-dask
Last synced: 12 months ago
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Dask-based utilities to process N5 images
- Host: GitHub
- URL: https://github.com/janeliascicomp/n5-tools-dask
- Owner: JaneliaSciComp
- License: bsd-3-clause
- Created: 2024-02-07T01:11:25.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-11T17:16:21.000Z (over 1 year ago)
- Last Synced: 2025-01-01T05:29:04.443Z (about 1 year ago)
- Language: Python
- Size: 599 KB
- Stars: 1
- Watchers: 6
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# n5-tools-dask
Dask-based utilities to process N5 images. This repo is a proof of concept and is not meant to be used for production purposes.
## Usage
1. Load the dependencies
```
conda env create --file environment.yml
conda activate n5-tools-dask
```
2. Run any of the scripts
```
mkdir output_tiffs output_n5
python src/n5_to_tif.py -i data/test.n5/ -d mri/c0/s0 -o output_tiffs
python src/tif_to_n5.py -i output_tiffs -o output_n5 -d mri/s0 -c 64,64,64 --compression gzip
python src/n5_multiscale.py -i output_n5 -d mri
```
This will reprocess the included n5 into a series of TIFFs, which are then reprocessed back into an n5 with smaller chunking. Finally, it will add multiscale imagery.