zebrafish

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

The Virtual Brain Explorer (ViBE-Z) is a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. It automatically detects 14 predefined anatomical landmarks for aligning data. It also offers a database and atlas. The ViBE-Z database, atlas and software are provided via a web interface. A data preparation step is needed in order to provide the right input data and format.

Normalize the orientation of the images of the Zebrafish embryos.

In the documentation webpage, the aim of the workflow is to normalize the orientation of the images of the Zebrafish embryos, find the point of injection of tumor cells and measure the distribution of Cy3 stained tumor foci.

ImageJ macro implementation of the Workflow described in Ghotra et al (2012). Note that currently only the angle and orientation normalization is implemented in this version.

Sample images are linked in the documentation webpage. 

idTracker is a videotracking software that keeps the correct identity of each individual during the whole video. It works for many animal species including mice, insects (Drosophila, ants) and fish (zebrafish, medaka, stickleback). idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. Technique details and analyses of several applications are described in Pérez-Escudero et al (2014).

Video protocol: https://www.youtube.com/watch?v=oC9tp5TKAyw

Example image: Example video of 5 zebrafish