Blog – ImgLib2 and BigDataViewer projects

Lazy parallel processing and visualization of large data workshop at I2K 2024

tutorial

workshop

bdv

imglib2

fiji

visualization

hdf5

n5

zarr

bdv

spark

Workshop on developing lazy n-dimensional image processing workflows using ImgLib2, N5 for image I/O, BigDataViewer for image visualization, and Spark to parallelize it all on compute clusters.

Stephan Saalfeld, Tobias Pietzsch

N5 attribute paths

n5

attributes

metadata

tutorial

Learn to get and set arbitrary parts of an attribute hierarchy with the N5 API.

John Bogovic, Caleb Hulbert

N5 API Basics

hdf5

n5

zarr

imglib2

tutorial

Basics of the N5 API for Java developers. This tutorial shows how to read and write n-dimensional image data and structured metadata into HDF5, N5, and Zarr containers using the N5 API.

John Bogovic, Caleb Hulbert

Position and displacement field transformations

imglib2

transform

deformation

displacement

Create and apply non-linear transformations with ImgLib2.

How to add your project to the Ecosystem page

quarto

web

In this blogpost you will learn how you can list your project that leverage BDV or ImgLib2 on the Community Ecosystem webpage. First copy the template.qmd file found here an…

Adding Stream support to ImgLib2

imglib2

stream-api

java

Examples and a discussion on performance

Tobias Pietzsch

How to work with the N5 API and ImgLib2?

imglib2

java

n5

hdf5

zarr

jupyter

notebook

Read and write ImgLib2 data with the N5 API.

Stephan Saalfeld

How to display ImgLib2 data in a notebook

imglib2

jupyter

notebook

Render ImgLib2 data into notebook objects

Stephan Saalfeld

User-configurable Keymaps

ui-behaviour

bigdataviewer

How to set up user-configurable keyboard shortcuts using ui-behaviour and BigDataViewer’s Preferences Dialog

Tobias Pietzsch

Setup the IJava jupyter kernel

jupyter

ijava

jshell

java

kernel

Follow these instructions to setup the IJava jupyter kernel by Spencer Park.

Stephan Saalfeld

Juliaset Lambda

imglib2

lambda

fractal

juliaset

bigdataviewer

Interactively render the Juliaset as a lambda function in BigDataViewer.

Stephan Saalfeld