Software

Channels Plus

Channels Plus is a free & open-source channels tool for ImageJ/Fiji.

Channels Plus combines the functionality of the built-in Channels tool and B&C tool, which are frequently used together. It presents separate histogram and minimum/brightness/maximum level controls for each channel, plus per-channel solo and mute controls. It is designed to streamline workflows for multi-channel (e.g. fluorescence) images.

Installing Channels Plus:

The plugin can be quickly installed via the project’s ImageJ update site. Please refer to the tutorial on how to add the Chanels Plus update site to your Fiji installation. The update site has the following URL: http://sites.imagej.net/Channels-Plus

Source code: on GitHub

WebcamJ

WebcamJ is a free & open-source webcam plugin for ImageJ/Fiji.

WebcamJ captures still images (snapshots, montages and stacks) from the camera's compressed live-feed, directly into ImageJ/Fiji. The live view offers configurable crosshair, grid and graticule overlays.

WebcamJ can be used in conjunction with webcam-enabled microscope cameras, from inexpensive USB microscopes to microscope-mounted Backbone-modified GoPro HERO8+.

Installing WebcamJ:

The plugin can be quickly installed via the project’s ImageJ update site. Please refer to the tutorial on how to add the WebcamJ update site to your Fiji installation. The update site has the following URL: http://sites.imagej.net/WebcamJ/

Source code: on GitHub

Atlas Toolkit

We developed this software to integrate 3D imaging datasets that encompass different aspects of eye development, such as gene expression profiles, signalling pathway activities, cell dynamics and tissue geometry.

Atlas toolkit is a Fiji/ImageJ plugin for fast group-wise registration of 3D morphological datasets that does not rely on landmarks.

Paper: Grocott, T., Thomas, P., Munsterberg, A. (2016) Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks. Scientific Reports Full Text

ImageJ Wiki: http://fiji.sc/Atlas_Toolkit

Source Code: on GitHub

Instructional videos

This video shows how Atlas Toolkit can be used to align (register) multiple image stacks together.

This particular tool generates two different outputs: 1) the aligned image stacks, and 2) an '.ots' file for each of the aligned image stacks.

The '.ots' file records the alignment process so that it can be repeated later.

This video shows how Atlas Toolkit can use the '.ots' files to reproduce a particular alignment. At the end of the video you can see a direct comparison of the same stack 'before' and 'after' alignment.

This is useful when you want to repeat an earlier alignment, but using different data channels from the same input image stack.

For example, say you aligned two or more tissues after labelling them - you could then apply that exact alignment to the raw image stacks, or to different processed versions.

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