Working with Cell Array, Indexing

I'm working on doing some image analysis and I want to be able to manipulate the pixel data.

I have multiple channels (channel1, channel2, channel3) which correspond to pixel data of the image for different laser colors. I'm working with confocal microscopy. Specifically with a Z-stack image.

So far I can put the data that I want to analyze into a cell array.

For example, channel1 is a 44x1 cell. All channels for a certain image will be the same length. However different images won't necessarily be 44. They could be nx1

channel1 is a 44x1 cell. It contains matrices that are 2048x2048 which contain the pixel information

2048x2048 uint16

2048x2048 uint16

...

2048x2048 uint16

I want to be able to take one of the matrices in the cell array and adjust the pixels within it. Then put it back in the same position in a new cell array.

So my issue is basically how to access the matrix in R1C1 of channel1, perform a manipulation of the pixel data in that matrix, and take that new matrix and put it into a new_cell_array in position R1C1.

Then repeat that procedure for the matrix found in R2C1 of channel 1 and put it in new_cell_array in position R2C1. And so on and so forth

Any help would be greatly appreciated

Answer 1

[José-Luis]

I am sorry, but I don't really understand how your data is structured. Are you having troubling addressing data in your cell array?

If so, please read this.

Answer 2

[Ben11]

When you say: However different images won't necessarily be 44. They could be nx1 do you mean that some stacks will contain 44 images and other n images?

If so it might be simpler to store every image (with all 3 channels) in a single cell, forming a cell array containing nx1 cells instead of 3 cell arrays of size nx1. You could then access the data of every image like so (and after looking at the link @José-Luis provided):

YourImage(Height,Width,Channel) = YourCellArray{i};

% Here Height = Width = 2048 and Channel can be either 1,2 or 3. i would be the index corresponding to the image you want to access in your cell array, hence could could implement a for-loop to modify each image in some way or use cellfun for example to apply a similar function on every image.

Is that what you meant?