Free and open source

OMERO.figure is an OMERO web application that makes generating figures from images in an OMERO image database very quick and easy. The images in the figure link back to the original data, greatly simplifying the process of adjusting the view and keeping track of original data. PDF documents are generated, which can be opened using e.g. Adobe Illustrator or Inkscape in order to produce the final finished figure.

The Fiji distribution of ImageJ comes with several manual tracking tools, two of which are particularly useful:

* _Plugins->Tracking->Manual Tracking_

* _Plugins->Tracking->Manual tracking with TrackMate_ (TrackMate is an advanced automatic tracking tool, with the option for manual editing of tracks)

The _Manual Tracking_ plugin is quick to use, intuitive and produces easy-to-understand output. TrackMate has the advantage that automatic detection and linkage can be combined with manual input.

Update sites

MtrackJ (see the component page here) can be installed via Fiji update sites. It has many shortcut keys enabled so for manually tracking many data, it will become quite efficient as you get used to the short-cut key operation.

Pre-processing

Pre-processing steps before manual tracking might include:

* denoising and/or deconvolution

* flicker and photobleaching correction, e.g. using Fiji's _Image->Adjust->Bleach Correction_

* flat-field correction, and/or bandpass (ImageJ's _Process->FFT->Bandpass filter_) according to the size of the features of interest

Image processing library for Python >The scikit-image SciKit (toolkit for SciPy) extends scipy.ndimage to provide a versatile set of image processing routines. It is written in the Python language. This SciKit is developed by the SciPy community. All contributions are most welcome!

This protocol takes a folder containing images as input and extract each channel in a separate sub folder.

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.