Bioactivity Recorder v5.91

Data aquisition and analysis software for L-Card and National Instruments cards. Works as single- or multichannel chart recorder and spike detector for electrophysiology (intracellular, extraellular, ECG, EMG...).

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Apoptosis correlator (download java, class)

Plug-in for ImageJ to calculate necrosis/apoptosis/live cells ratio in cell culture images.

Cell viability in culture can be determined utilizing the vital fluorescence assay (Mironova et al, 2007).  Confocal or fluorescent images of cells after staining of all nuclei with acridine orange and dead cell nuclei with ethidium bromide can be processed by Apoptosis Correlator to calculate the ratio of necrotic, apoptotic and live cells. This plug-in is a modified version of Image Correlator by Wayne Rasband and Kevin Baler.

Apoptosis correlator requires two images representing red and green fluorescence of cells simultaneously stained with acridine orange and ethydium bromide. Images must be the same XY size and 8 bit grayscale color depth.

Apoptosis Correlator

You can select the noise threshold to eliminate too “dark” pixels from calculations. The threshold value can be determined automatically using ISODATA algorithm (Ridler, Calvard, 1978) implemented in ImageJ. The algorithm selects lowest initial threshold and iteratively increases it until resulting threshold = (average background + average objects)/2.

Display nonzero counts list checkbox allows showing the Excel exportable list of correlating pixels suitable for further analysis.

Apoptosis correlator generates an XY plot showing correlation of two images. It takes the value of a each pixel in the first image as the x-coordinate and the value of the corresponding pixel in the second image as the y-coordinate. On the resulting image non-correlated pixels looked green and red and were attributed to live and necrotic neurons, correspondently. Correlated pixels looked yellow-orange and were attributed to nuclei of apoptotic neurons.

The resulting correlation plot will show the distribution of correlated pixels separated in four parts with the noise threshold lines.

The text window will show ratio of pixels corresponding to three image segments representing pixels occupied by live, necrotic and apoptotic cells.

Installation: Put Apoptosis_Correlator.class to ../ImageJ/plugins/


  • Ridler T, Calvard S, Picture thresholding using an iterative selection method. IEEE Trans. Systems Man Cybernet., vol. 8, pp. 630-632, 1978.
  • Mironova EV, Evstratova AA, Antonov SM. A fluorescence vital assay for the recognition and quantification of excitotoxic cell death by necrosis and apoptosis using confocal microscopy on neurons in culture. J Neurosci Methods. 2007 Jun 15;163(1):1-8. Epub 2007 Feb 20.