DNA damage


This workflow will batch process a directory of images: - comets should be horizontally oriented, tails to the right. Additional preprocessing is required if the gel does not match with this orientation (Rotate images, Using ImageJ/Transform Image or TransformJ plugin for example). Then using the plugin:

  1. Uneven background correction
  2. Automatic detection of comet shapes with outliers detection
  3. Automatic detection of the heads of comets (brightest region or profile analysis)
  4. Statistical values of tails, heads and Olive moments.
  • Manual correction is available.
  • Does live analysis with Micro-Manager


This is a simple example of a DNA damage assay using single cell gel electrophoresis. Here, the measurement of interest is the length and intensity of the comet tail. Also, illumination correction is used to reduce background fluorescence prior to measurement. Also shown is a silver-stained comet example in which the percentage of DNA contained in the tail is calculated.

Example Images: Packaged together with the cellprofiler pipeline file. 


Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.