2D

Simple macro to separates blobs.

• Load the ImageJ sample image "Blobs"
• Run the plugin Morphological Segmentation
• Display the overlaid

This macro depends on "Morphological Segmentation" component of the MorphoLibJ library, which should be installed via update sites.

This macro was designed to measure the size of the scratch wound in a wound scratch assay. It uses an edge-detection and thresholding technique.

It will batch process all images in a directory. Images captured by time-lapse should be compiled into stacks using a tool similar to "Metamorph nd & ROI files importer (nd stack builder)" by Fabrice P. Cordelières. Images to be analyzed should be placed in one directory (Source Directory). A second directory should be created to save results files and images (Destination Directory). Setting correct Lower and Upper thresholds is important to obtain a good result. Two macros are available, one using edge detection, the second one using background subtraction.

It explains how to use ImageJ to compare the density (aka intensity) of bands on an agar gel or western blot.

Some notes can be found here: http://cellnetmcweb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf

The workflow contains a Matlab package (plusTipTracker) for segmentation and tracking of microtubule tips, based on fluorescence time-lapse movies from microtubule tip markers such as EB-GFP. The tracking model accounts for the specific movement characteristics of microtubules Moreover, scripts for secondary analysis of detected microtubule paths are provided.

plusTipTracker is part of u-track 2.0 package. The workflow is described in the reference. 

An exponential curve fitting library used for Fluorescence Lifetime Imaging (FLIM) and Spectral Lifetime Imaging (SLIM), available as:

• Source code as C/C++ and Java library

• ImageJ plugin

• Standalone Open-Source Windows application

Publications:

• Barber, P.R., Proc. SPIE, 5700, 2005.pdf
• Barber, P.R., J. R. Soc. Interface, 6, 2009.pdf