Foci Counter

Cells with chemically induced DNA damage sites, Red (Foci): 53BP1, Green (Marker): CyclinA, Blue (Segmentation): Hoechst staining

Foci Counter / Colocalization Counter

The macro evaluates for each cell core the presence of an optional marker, counts the foci in up to two different channels and performs a colocalization between the foci channels.

Usage

The macro works on multichannel images containing at least one channel for segmentation of objects and one channel in which the foci are counted. Optionally, colocalization with a second foci channel and the presence of a marker can be evaluated. A detailed manual guiding through the single steps of the macro can be downloaded on the right side.

Technical Info

Core segmentation is done via an automatic thresholding method on the median filtered (r=2) core channel. To correct the background in the damage channels a median (r=30) filtered duplicate was substracted. DNA damage foci are identified using the ImageJ Find Maxima command. Noise parameters are adjusted for each channel.
Two foci are considered as colocalized when the distance between them is at most 2 pixels. ina ddition intensity based colocalization measures (pearsons/manders) are calculated with the ImageJ plugin JACoP.

Foci Projected Measurer

Extracts regions of interest from one channel and measures the intensity on another channel. Stacks are Z-projected.

Usage

The macro works on multichannel image stacks containing at least one channel for segmentation of objects and one channel in which the foci are counted. Optionally, the presence of a marker can be evaluated

Foci Counter/Measurer Options

  • Threshold Method: Automatic threshold method used to threshold the core channel.
  • Core Channel: Color of the core channel.
  • Marker Channel: Color of the marker channel.
  • Foci Channel: Color of the first and second foci channel.
  • Find Maxima Score Big: Noise value for the Find Maxima function of ImageJ. Higher values result in selection of bigger focis.
  • Find Maxima Score Small: Noise value for the Find Maxima function of ImageJ. Lower values result in selection of smaller focis.
  • (Create 'Find Maxima' settings image): Only does the preprocessing.