2D

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

ImageJ plugin to analyze changes in vessel diameters, described in Fernández er al (2014). More specifically the paper describes the measurement of isolated retinal arterioles (ca 50 micrometer diameter) but can be used for diameter measurements of similar vessel structures.

Variational algorithms to remove stationary noise. Application to microscopy imaging. This plugin allows to denoise images degraded with stationary noise. Stationary noise can be seen as a generalization of the standard white noise. Typical applications of this plugin are:

- Standard white noise denoising using a total variation and fidelity term minimization. Even though total variation denoising is not the state of the art (regarding SNR improvement), it may be very valuable for further tasks such as image seg- mentation).

- Destriping (the problem that motivated us to develop these ideas). 

- Deconvolution (even though most users won't be able to use this feature).

- Cartoon + texture decomposition which might be useful to compress images, analyse textures or simplify segmentation like tasks.

An automated MATLAB tool for segmentation of surface stained cells

A clear tutorial on how to write a MATLAB script to segment clustered cells.

The full script is downloadable near the bottom of the article.