====== HeatMap From Stack ======

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

===== Description =====
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: http://www.samuelpean.com/how-substract-background-video-imagej). In output you will have a graph and a table with the numerical score of each sub-area.

{{ :plugin:stacks:heatmap_from_stack:heatmap_from_stack_mini.png | 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. 

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

===== Download =====
http://www.samuelpean.com/heatmap-from-stack (You will find a commented and animated demonstration in this page too).

===== License =====
GPL