I need a bit help with image processing and exporting data to excelsheets

I want is to quantify different parameters for every induvidual mitochondrion in the cell. My supervisor has told me to replicate his protocol in MatLab: https://doi.org/10.1002/cyto.a.20198

I have replicated all the image processing and enhancement steps, and turned the picture into Binary: (see picture)

The two cells here has not been masked, but I will deal with that later (found a solution I will implement).

Now I want to extract data, and I used the following code:

%%Label items for quantification
[mitLabel, mitNum] = bwlabel(Ibin);
%Set parameter
mitStats = regionprops(mitLabel, 'All');
%Extract arrays for area, perimeter, major axis length and minor axis length for each element in binary image
mitArea = [mitStats.Area];
mitPerimeter = [mitStats.Perimeter];
mitMaxL = [mitStats.MajorAxisLength];
mitMinL = [mitStats.MinorAxisLength];

I am processing a unknown amount of images that varies with each experiment, so I simply cant define which columns and rows I want MatLab to fill specifically.

So I need a a code that adds a new variable Cn+1 (Cell numer n +1) to the adjacent cell Cn(Cell nr n) for every picture of cell that is processed, I also need it to the same for every mitochondria thats in the cell:

     C1 | C2 | C3 | C4 | ...Cn
 M1          data
 M2
 M3         data
 M4
 ..
 Mn

I want one excel-sheet for each parameter, such as area, perimeter, major axis lenght, minor axis lenght etc. I also need to convert pixels to micrometer unit, so if there is any good way to do this, that would be great. I also need to exclude elements smaller than what I specify.

I hope this explained it a little better. Thanks.