Linux

These two KNIME workflow solutions are similar: first one detects nuclei and spots inside the nuclei without taking care of surrounding regions, i.e. mitochondria. The second one provides the full solution including spots in mitochondria.

see section 2.4 for KNIME workflow. Section 2.3 is also available, using Fiji. 

Sample image: hela-cells.tif (674k x 3)

For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.

This protocol perform a median filter on the active sequence using the ImageJ rank filter plugin. Then, it converts the result back into Icy for display.

An example showing passing data between ICY and ImageJ using ImagePlus object. 

This tool adds to ImageJ functions to build and organize montages. It comes with the ImageJ installer but can also be downloaded from the ImageJ wiki. A video tutorial is available.

CellX is an open-source software package of workflow template for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images with distinguishable cell boundary.

Installation and step-by-step usage details are described in Mayer et al (2013). 

After users provide a few annotations of cell sizes and cell boundary profiles, it tries to match boundary profile pattern on cells thus provide segmentation and further tracking. It works the best on cells without extreme shapes and with a rather homogeneous boundary pattern. It may not work well on images with cells of sizes only a few pixels. Its output comprises control images for visual validation, text files for post-processing statistics, and MATLAB objects for advanced subsequent analysis.