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HeatMap From Stack


Samuel Péan (based on M. Austenfeld Count_Stack_Pixels plugin and Michael Doube Thermal LUT)


This plugin is a qualitative AND QUANTITAVE method to calculate the preferential place of an individual or a group from a stack (= video converted as an image sequence). Detection of the individual(s) is based on the grayscale value. So I strongly recommand you to subtract background from your image sequence to avoid bias (tutorial here: In output you will have a graph and a table with the numerical score of each sub-area.

 HeatMap From Stack

About the calculation methods:

- Absolute: all the results are divided by the number of frames. So a red point in the heatmap means that this point was black during all the sequence (=100% of occurence). This method can be use when you have a high density of individual in your studied arena.

- Relative: all the result are divided by the highest score found. For example, in the animated demonstration, we have only 6 individuals in the arena, so it's nearlly impossible to have a part of the tank occuped during 100% of the time (exept in case of total immobility). Absolute method isn't adapted in this case, it's much better to use the Relative one: the best score will be the reference.

- Log10: once you have chosen your calculation reference, you can apply a Log10 transformation.


Copy Thermal.lut file in your imagej/luts folder and the HeatMap_From_Stack.class file in your imagej/plugins folder.

Download (You will find a commented and animated demonstration in this page too).



plugin/stacks/heatmap_from_stack/start.txt · Last modified: 2019/04/12 13:13 by

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