fmeyenhofer / aba_j

Brain atlasing toolkit for ImageJ

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ABA-J is an ImageJ plugin to register 1 single or a series of subsequent histology sections to the Allen Brain Atlas (ABA), an online resources providing a reference space, annotations and access to many mapped genes. Once the section images are registered to the reference atlas, the plugin allows to retrieve annotations and use them as regions of interest (ROI's).

Acronym	Description
CCF	Common Coordinate Framework
ARA	Allen Reference Atlas

Installation

To use the plugin you need to download and install ImageJ first. We recommend the Fiji distribution, shipping with a collection of plugins that will be useful in this context.

Plugin installation in ImageJ

You can download the binary version of the plugin as jar-file on the releases page. For the installation of the plugin please refer to the ImageJ documentation how to install 3rd party plugins on the official wiki.

Plugin compilation from source

To compile the source code and package it into a jar, that can be imported in ImageJ, clone this repository using Git. Then the jar can be easily packages using Maven with the command mvn package.

Usage

Once installed in Fiji, you can access a collection of functions through Main Menu > Plugins > Allen Brain Atlas

Note: This neuroinformatics plugin performs computationally intense operations and deals with a considerable amount of data (input and web resources). Therefore the users are advised to run the software on a adequate machine with a configuration that fulfils the following requirements:

• fast internet connection (LAN)
• a good CPU
• enough memory (at least 8 GB)

aba_j's Issues

Change default atlas parameter for InteractiveAlignment

10um, annotation volume takes (too) long.
25um avg. template might be a better choice to start.

Add shortcut in the InteractiveAlignment BDV to save the transformation

Remove the SHIF-U shortcut and use something like CMD-S. This should:

• save the .map-file if the image path of the input section images can be retrieved
• ... or bring up a dialog to define a output path
• in any case show a message in the BDV once the file was saved