I took z stack images with a microscope. Can I read them in as z stacks and Matlab convert them to single combined image with range?

Hello!

I have an image taken with z stacks (image taken with a confocal that measures an area at different focal lengths), I would like to do the equivalent as done in imagej with z project which is to load the z stack image and create a 2d image from the z stack image. How can I do this? Can this be done with multiple z stack images at once? The 2d composite image would have a greater depth of field (i.e. the thickness of the plane of focus) than any of the individual source images

Thank you very much!

neo

Answer 1

[Image Analyst]

If you want a 3-D volumetric image you can do

image3d = cat(3, image1, image2, image3, image4, etc)

[Neo]

I have the volumetric image I want to condense it to a 2d image with depth combination of its predecessor. Thank you!

[Image Analyst]

I don't know what that means. Do you just want to use mean(), max(), or min() along dimension 3? Or do you want to basically go through each slice taking the best, sharpest, most in-focus pixels from that image?

[Neo]

I have the volumetric image, I want to condense it to 2d without losing the quality (i want to combine all of the focal depth of the 3d image into a 2d image).

[Neo]

@Image Analyst the latter of what you have written.

[Image Analyst]

I don't have any code for that. You'll have to check the File Exchange or somewhere else.