plugin

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.

LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation

Download instruction:

There is no download but you can easily install this plugin via ImageJ update site. If you reallu need to download the jar file, access the file in the update site repository (Link)

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

CEM runs as an imageJ plugin with an optional Matlab extension to remove cell bodies. More details are published at Kerman et al. 2015 Development. Supplemental Material includes a detailed user manual and the download link.

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.