From 5430a5edd13b691dbb8a29d2efc6b3c81a45d0e3 Mon Sep 17 00:00:00 2001 From: Stephan Saalfeld Date: Wed, 4 Sep 2024 15:22:03 -0400 Subject: [PATCH] doc: update README.md --- README.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 78b70d5..b815b0f 100644 --- a/README.md +++ b/README.md @@ -2,13 +2,18 @@ # 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. @@ -18,7 +23,7 @@ Install into your favorite local binary `$PATH`: ``` 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 @@ -31,7 +36,7 @@ n5-view \ -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