README.md

APR-ImageJ

APR-ImageJ provides support for Adaptive Particle Representation (APR) in ImageJ/Fiji.

Available commands

File -> Import -> APR...

Imports APR file to ImageJ. It reconstructs whole image from APR representation to pixel based (standard ImageJ stack).

File -> Export -> APR..

Exports pixel based image to APR format. Parameters:

• Intensity Threshold - values below this threshold will be ignored, this is useful for removing camera artifacts
• Minimal SNR - minimal ratio of the signal to the standard deviation of the background
• Lambda - gradient smoothing parameter (reasonable range 0.1-10)
• Minimum signal - minimum absolute signal size relative to the local background, useful for removing background
• Relative error - maximum reconstruction error relative to local intensity scale (reasonable range 0.08-0.15)

Note1: set value of parameter(s) to -1 for automatic detection of best possible values.

Note2: extension _apr.h5 is added to exported file name.

Plugins > APR > APR (BDV) viewer

Opens APR image in BigDataViewer using LibAPR-java-wrapper to show Adaptive Particle Representation (APR) files. Thanks to reconstruction 'on the fly' it allows to open bigger files that memory available on the machine.

Plugins > APR > APR (BVV) viewer

Opens APR image as a volume. This command is based on BigVolumeViewer.

Note: this plugin requires BigVolumeViewer already installed in your ImageJ. This can be done by Help->Update->Manage update sites and adding there BigVolumeViewer Demo to your active updtee sites.

How to download, build and install

Download source code of APR-ImageJ

git clone --recurse https://github.com/AdaptiveParticles/APR-ImageJ.git

Build plugin (might take a while)

Note: Java 1.8 is required

cd APR-ImageJ
mvn package -Dmaven.test.skip=true -Dmaven.javadoc.skip=true

Manual installation in ImageJ/Fiji

• copy result jar file from ./AprImageJ/target/AprImageJ-0.0.1-SNAPSHOT_Full.jar to plugins directory of your ImageJ installation, on Mac/Linux:

cp ./AprImageJ/target/AprImageJ-0.0.1-SNAPSHOT_Full.jar   /my/app/dir/Fiji.app/plugins

• also make sure that you have javacpp-1.4.1.jar in jars directory (can be found in .m2 directory of your home), it is needed since javacpp shipped with Fiji is too old:

cp ~/.m2/repository/org/bytedeco/javacpp/1.4.1/javacpp-1.4.1.jar /my/app/dir/Fiji.app/jars/

Contact us

If anything is not working as you think it should, or would like it to, please get in touch with us!!!