Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark

Setup instructions

conda

java

ijava

jupyter

quarto

How to get started …

Stephan Saalfeld

ImgLib2 is lazy

imglib2

jupyter

notebook

… very, very lazy, like … everywhere!

Stephan Saalfeld

N5 API

imglib2

java

n5

hdf5

zarr

jupyter

notebook

Read and write ImgLib2 data with the N5 API.

Stephan Saalfeld

Lazy image processing with ImgLib2 cache

imglib2

jupyter

notebook

cache

lazy

cell

… by defining the processing operations over cells.

Stephan Saalfeld

Using the ImgLib2 blocks API

imglib2

java

n5

jupyter

notebook

Using the ImgLib2 blocks API for downsampling and convolution

Tobias Pietzsch

Lazy processing with ImgLib2 and Spark

imglib2

jupyter

notebook

spark

Working around (lack of) serialization.

Stephan Saalfeld

Procedurally generated image

We define the Juliaset as a function in 2D real space using a BiConsumer lambda function. The BiConsumer receives two parameters, the first one (x) is the 2D coordinate, the…