automation of Ca imaging data analysis

[Kirill Ukhanov]

Dear all,

I wonder if anyone has thought or perhaps developed a routine to do
semi-automatic cell detection analysis in the time series of images
acquired from a large (100+) population of cells. Having a reference
stimulation at time X would allow to select all the responding cells of
interest and assign ROIs for each of them. Then ImageJ runs multiple ROI
measurement and outputs dF/Fo to the spreadsheet. People have
implemented  a similar algorithm in Matlab but for me it is hardly an
option.

thanks for your input

Kirill

[6:1135]

Hi, I've worked on a similar project (I think).
From the stack (t):
- median filter
- max projection (image / stacks / z max-project ...)
- thresholding
- particle analysis, keeping only the regions of interest
- add to the ROI manager
- plugin/ stacks T functions/delta F