Awesome

IMPORTANT NOTE The python code has been extracted into a imglib/imglyb. This repository contains Java code only now. To install the python package from conda, run

conda install -c conda-forge imglyb

imglib2-imglyb

imglib2-imglyb gives access pointers into native memory and expose them to ImgLib2 data structures. This means shared memory between native code, e.g. numpy in Python, and ImgLib2, i.e. any ImgLib2 algorithm can run on native arrays without creating copies of the data! For example, Python users can now make use of the BigDataViewer to visualize dense volumetric data.

Installation

imglib2-imlgyb is available on the saalfeldlab maven repository. Add this to your pom.xml:

<repositories>
    <repository>
        <id>saalfeld-lab-maven-repo</id>
        <url>https://saalfeldlab.github.io/maven</url>
    </repository>
</repositories>

<dependencies>
    <dependency>
        <groupId>net.imglib</groupId>
        <artifactId>imglib2-imglyb</artifactId>
        <version>${imglib2-imglyb.version}</version>
    </dependency>
</dependencies>

Build

cd /path/to/imglib2-imglyb
mvn clean package