HeatMap From Stack is a plugin for ImageJ. As ImageJ, HeatMap From Stack is FREE and Open Source.

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). The output are a graph and a table with the numerical score of each sub-area.

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. 

 See the commented demonstration

 Download plugin & sources !


 Download the archive file and extract it in your ImageJ plugin folder (usually C:Program FilesImageJplugins for Windows). Then restart ImageJ or use Help > Refresh Menus.


 To use the Thermal LUT, you must extract the files from the ZIP archive and then copy-paste the Thermal.lut file in the ‘ImageJluts’ folder.