bogovicj

emboBioImage2023_registration

Materials for the advanced image registration section of the "Advanced methods in bioimage analysis" EMBO 2023 course

imglib2-ij

Translation between ImgLib & ImageJ data structures (both 1.x and 2)

ome-ngff-java

Metadata stubs of the NGFF specification in Java

Beamer-Theme-Janelia

A minimalist and modern Beamer theme

bigdataviewer-biop-tools

Another repo for bdv tools.

bigdataviewer-core

ImgLib2-based viewer for registered SPIM stacks and more

bigdataviewer-vistools

Helpers to use BigDataViewer as a quick visualization tool in other projects.

bigdataviewer_fiji

Fiji plugins for starting BigDataViewer and exporting data.

bigwarp

A tool for manual pointwise deformable registration using bigdataviewer.

bogovicj.github.io

fiji-scripts

A wild collection of useful and partially broken scripts for Fiji and TrakEM2

ijp-imagetoatlas

2D sections to 3D atlas registration with Fiji and QuPath

imglib2

A generic next-generation Java library for image processing

imglib2-algorithm

Image processing algorithms for ImgLib2

imglib2-cache

Cache interfaces and java.lang.ref based implementation.

imglib2-realtransform

imglib2-roi

Regions of interest (ROIs) and labelings for ImgLib2

JaneliaDataStandards

A central hub for Janelia's bioimaging schemas, standards, and data formats.

mobie-io

mobie-viewer-fiji

multiview-reconstruction

Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

n5-utils

simple standalone BigDataViewer for multiple N5 (or HDF5) datasets

n5-viewer

BDV-based tool for visualizing multichannel multiscale N5 datasets.

ngff

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

numcodecs

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

openorganelle-blog

Periodic content for openorganelle

ossi-website

Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.

pom-scijava

Friendly base POM for all SciJava-based software

scijava-common

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

scripts

some shell scripts