Pixel intensity of image stacks

[anfleisch]

I have acquired 128x127 sized frames from a high speed CCD in png format within a folder (I can change the acquisition format if necessary). I would like to select an ROI or individual pixel and extract the pixel intensity data for that same region from each image. I have about 155 frames per second for 15 seconds, so I am dealing with close to 2500 frames. I know some programs let you work with stacks? What is the most practical way to accomplish this quickly? I will need to be able to do some data manipulation to the entire set. I may require some light spatial or temporal filtering. But mainly, I will need to transform the data from raw intensity to relative intensity using a least squares fitting. I suppose the biggest issue is just acquiring the data from the ROI/pixel from different frames quickly. 

[charris]

anfleisch:

I'll admit up front that I'm not too familiar with the conversions you're trying to do (you probably know the actual math better than I do), but I think you should be able to do it with the normal PNG Read functions. If you go into the functions palette, it's located in "Graphics & Sound --> Graphics Formats."

That will give you the image data (bit representations for each pixel will depend on the bit depth of the PNG) in a format where you can work with it on a pixel-by-pixel basis.

That covers opening one file and getting at the pixel data. If you want to open multiple files, we'll ideally need a clever way to automate it. In any case, we'll need a filename or reference for each file. Are the files named in some sort of pattern? If so, we can potentially build a filename string and have it increment (if it's a numeric value) upwards until we're out of files. You can use the "Path to String," "String to Path," "Build Path," and "Strip Path" functions for constructing file paths and inserting filenames.

Hope that helps!