Automated

A Jython script using the plugin : Register Virtual Stack Slices It takes a sequence of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas). One of the images in the sequence can be selected by the user as reference and it will remain intact. The plugin can perform 6 types of image registration techniques: - Translation - Rigid (translation + rotation) - Similarity (translation + rotation + isotropic scaling) - Affine - Elastic (via bUnwarpJ with cubic B-splines) - Moving least squares All models are aided by automatically extracted SIFT features.

The rapidSTORM project is an open source evaluation tool that provides fast and highly configurable data processing for single-molecule localization microscopy such as dSTORM. It provides both two-dimensional and three-dimensional, multi-color data analysis as well as a wide range of filtering and image generation capabilities. The general operation of rapidSTORM is described in Wolter et al (2012).

(from the webpage) >This usage example shows how to produce two-color images from spectrally unmixed data sets. It was written for an Alexa647/Alexa700 measurement on the Würzburg 1 biplane setup as documented in [Aufmkolk2012]. The first two tasks in this example produce prerequisite knowledge for the image generation, the alignment information (Produce linear alignment matrix) and the F2 ratios, i.e. the relative intensity of fluorophores between the channels. [Aufmkolk2012] Hochauflösende Mehrfarben-Fluoeszenzmikroskopie. Sarah Aufmkolk. Julius-Maximilians-Universität Würzburg. 2012-mar.

The ImageJ pligin, called PixFRET, allows a simple and rapid determination of channel bleed-through parameters and the display of normalized FRET images. see 2521

Input data type: 

Stacks with 2 channels (controls for bleed-through calculation) or 3 channels (FRET calculation)

Output data type: 

One Image with FRET values and One image with normalized FRET values

This macro is a plugin macro to the "Intelligent Imaging" workflow. It detects the Cytoo patterns (specific fluorsecence channel) and computes the occupancy (number of cells) of each pattern by analyzing the images of the DAPI channel. The analysis function can be easily extended to, for instance, only select the cells that are well spread on the patterns (by analyzing a third channel with a properly chosen marker of the cytoplasm).