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doc: update README.md
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axtimwalde authored Sep 4, 2024
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# n5-utils

Simple standalone BigDataViewer for multiple N5 (or HDF5) datasets
or mipmap pyramids and also a copy, rechunking, and recompressing
tool for N5 and HDF5.
https://github.com/user-attachments/assets/62d3415e-7f7c-4b43-886f-5e6de8a5b8a1

Installation requires maven, OpenJDK8, and lib-hdf5, on Ubuntu:
Collection of standalone command line tools to work with HDF5/ Zarr/ N5 datasets. Including:

- A simple standalone BigDataViewer for multiple datasets or mipmap pyramids.
- A copy, re-chunking, and re-compressing tool for individual datasets or groups.
- A `unique` tool to get the set of unique numbers in a dataset.
- An `equals` tool to compare two datasets.

Installation requires maven, OpenJDK, lib-hdf5, [and libblosc] on Ubuntu:
```bash
sudo apt-get install openjdk-8-jdk maven hdf5-tools
sudo apt-get install openjdk-21-jdk maven hdf5-tools libblosc1
```
On other platforms, please find your way and report back if interested.

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```
All dependencies will be downloaded and managed by maven automatically.

This installs two tools, `n5-view` and `n5-copy`.
This installs the tools, `n5-view`, `n5-copy`, `n5-equals`, and `n5-unique`

Run the viewer
```bash
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-c -1,1 \
-r 1,1,10
```
to look at two datasets or mipmap pyramids from an HDF5 and an N5 container at 1x1x10 resolution and contrast ranges [0,255] and [-1,1]. The viewer maps both contrast ranges into [0,1000] because BDV cannot yet deal with negative intensities and the sliders only show integers. Sorry for the hack.
to look at two datasets or mipmap pyramids from an HDF5 and N5 container at 1x1x10 resolution and contrast ranges [0,255] and [-1,1]. The viewer maps both contrast ranges into [0,1000] because BDV cannot yet deal with negative intensities and the sliders only show integers. Sorry for the hack.

Copy from N5/HDF5 to N5/HDF5:
```bash
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