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HomeHomeXTensionsXTensionsRequestsRequests#077 XTENSION REQUEST - batchanalysis#077 XTENSION REQUEST - batchanalysis
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#077 XTENSION REQUEST - batchanalysis
 
Hi all I would like to have something like a little macro for my analysis. My analysis is nothing fancy and pretty standard. However I have to analyze multiple pictures and it is always the same procedure of steps, hence I would like to automatize these steps. However, I have no experience with how to incorporate a pipeline of commands in Matlab or Python and therefore need your help. Does anybody have a suggestion on how I could do that? Here is what my analysis contains: I have 2 channels, one containing labeled matrix, and one containing labeled cells. I want to know how many cells have contact with the matrix and how big the contact area is. Mannually I perform the following steps: 1. Background subtraction in the channels 2. Select a region of interest ->Using the drawing mode to create a surface and mask all the channels 3. Create surfaces for the cells and the matrix 4. Calculate how many cells have contact with the matrix 4a. Create a binary channel, in which the channel of the matrix is masked with the matrix-surface 4b. Filter the cell-surfaces for an overlap with the binary channel 4c. Copy the statistics how many cells there are in total and how many are filtered 5. calculate the contact area 5a. Create another channel in which the binary channel is masked with the cell-surfaces 5b. create a surface in that channel 5c. Save the statistics for the surface area of these surfaces Except for the drawing of the ROI, which can only be done manually, it is always the same clicks in Imaris. I hope somebody has a good solution for me. Thank you already in advance.

 
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