2D

This method allows to compute a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose Moments in the list. In Aphelion, the tool is in Segmentation->Threshold->AphImgMomentThreshold The original paper is 2449

The QuimP software from Bretschneider group is deployed as ImageJ plugin and includes model-based cell segmentation, cell outline tracking and quantification of the spatially resolved speed of protrusions and retractions. The algorithm to calculate morphological dynamics is faster compared to other approaches (e.g. Machacek and Danuser, 2006). The reference paper describes the workflow for these analyses.

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

SlideToolkit is a collection of command-line tools to assist with the automated histology analysis of whole-slide images. The publication linked in the "reference" details the actual workflow. 

This includes tools to organize the data, perform tiling and subsequent batch processing of the generated tiles in a cell profiler pipeline. All the tools are designed to run on a single PC or on a HPC system. The scripts in the toolkit are on github under MIT licence.

A utility macro for the specified use of BioFormats plugin. Takes a folder of proprietary images formats (Zeiss zvi, lsm, czi or Nikon nd2) and extracts them to .tif images

The extracted images are located in a folder defined in the menu. Other options: reset spatial scales, reads ROIs, split channels, add stage position in the name.

note: The old name of the macro was "ZVI Extractor" and the data format was limited to ZVI, but the upgraded version includes more formats.

Requires Bio-Formats plugin