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n5-ij

ImageJ convenience layer for N5

n5-imglib2

n5-spark

Spark-driven processing utilities for N5 datasets.

n5-utils

simple standalone BigDataViewer for multiple N5 (or HDF5) datasets

n5-viewer

BDV-based tool for visualizing multichannel multiscale N5 datasets.

n5-zarr

Zarr filesystem backend for N5

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

ngff-transforms-prototype

A prototype implementation of NGFF transforms

numcodecs

A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.

ome-ngff-java

Metadata stubs of the NGFF specification in Java

ome-zarr-fiji-ui

GUI Dialog to show structure of an ome.zarr dataset and to allow the user to cherry-pick image of interest, in Fiji.

openorganelle-blog

Periodic content for openorganelle

paintera-conversion-helper

Script to assist conversion of n5 datasets to paintera-friendly formats

pom-fiji

The parent project for all Fiji projects

pom-scijava

Friendly base POM for all SciJava-based software

pygreentea

registrationworkflows_i2k_2020

Automatic and manual workflows course I2K 2020

render

Render transformed image tiles

schemas

Documentation of how data, metadata, and derived data are are organized for the COSEM project

scifio

SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.

scijava-common

A plugin framework and application container with built-in extensibility mechanism :electric_plug:

scijava-ui-swing

SciJava UI components for Java Swing.

scripts

some shell scripts

simpleelastix

Multi-lingual medical image registration library

skeleton2swc

spatial-image-ngff

Write out multi-scale spatial images in a Zarr-formatted Next Generation File Format (NGFF)

template_visualizations

trakem2-tps

Enables thin plate spline transformations in TrakEM2

transform-helpers

Helper tools and API to apply transformations to coordinates and images

transforms_tutorial

ImageJ examples for the 2019 DAIS Learnathon.