I need some help on spreadsheets in Matlab

I have written a script for analysing images of biological cells, which segments them and quantify the output.

Now I need to make Matlab write this information in a spreadhsheet.

This script utililizes the regionpropstool i Matlablab, and creates an array of information on each component like:

• Surface Are
• Perimeter
• MaximumAxisLength
• MinimumAxisLength

There is always an unknown amount of cells (Cn) that has an uknown amount of mitochondrion (Mn).

I need to make Matlabs add the following information to a spreadsheet:

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

The problems is that I dont know how to make Matlab add a new row or column, each time it processes a cell. So how does it assign a number to Cn and Mn

[Kevin Chng]

Write information to spreadshett

Typically, there are 3 ways

1) readtable(), you structure your information in table first, and then write it to excel or spreadsheet.

2) xlswrite(), write matrix to spreadsheet.

3) ActiveX, it is more flexible, it can change colour, or specific which coloumn or row number of spreadsheet to be written.

excel = actxsever('Excel.Application');
wb = excel.Workbooks.Open('somefile.xlsx');
ws = wb.Worksheets.Item('sheetname');
ws.Range('B2:B8').Insert;
.........

which one do you prefer?W ecan discuss further. You may further explain how is the flow of your logic? like what are you going to structur your data before writing them to spreadsheet.

[Guillaume]

You can make regionprops return a table directly which is trivial to write into a spreadsheet. However, it sounds like what you want is a bit more complicated and I'm a bit unclear on what you have.

Is regionprop applied to cells or mitochondria? I assume it's mitochondria. If so where do the multiple cells come in? What actual data would go into your example sheet. Obviously if have cells as columns, mitochondria as rows you can only have one of {'Area', 'Perimeter', 'MajorAxisLength', 'MinorAxisLength'} inside the spreadsheet cells. Would the other ones go into different sheets?

Perhaps it would be a good idea for you to attach an example mat file that shows what form your results actually take.

[August Hoel]

Thanks for your answer! I will attach an example when I am at work tomorrow, and elaborate a bit more :)

[Guillaume]

August Hoel comment mistakenly posted as an answer moved here:

Hey again, what 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)

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 x +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.

[Guillaume]

Thank you, your explanation is much clearer. I do something similar for my work except that I look at images of droplets. I have an unspecified number of images each with a varying number of droplets.

What I don't particularly understand is your proposed storage. Wouldn't each cell (image?) has a varying number of mitochondria? In that case, it doesn't really make sense to have the storage you propose, which is in effect a 3D array (Cell x Mitochondria x paremeter). In my opinion, you would be better off using a 2D storage where each row is a mitochondria, and the cell it comes from as another parameter. Something like:

Mitochondria  |   Cell   |  Area  |   Perimeter   | MajorAxis |  MinorAxis
     1              1        xxx        yyyy          zzzz        ccccc
     2              1        xxx        yyyy          zzzz        ccccc
     3              1        xxx        yyyy          zzzz        ccccc
     1              2        xxx        yyyy          zzzz        ccccc
     2              2        xxx        yyyy          zzzz        ccccc
     1              3        xxx        yyyy          zzzz        ccccc
  ....

With regards to conversion from pixel to micrometer, this really warrant its own question. To do this you need to know the scale of your images. You know this either by taking an image of an object of known size under the same imaging conditions, or you know this becaue you know the magnification of your imaging system.

[August Hoel]

Thanks, I was also suggested by some other people that this was the best way to arrange the data. I however have a problem with making MatLab do the following. How do I import:

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];

Is it better to use an array, or MatLab table? How do I get it to assign each Mitochondrion a new string variable (M1, M2...Mn), when there is an unknown amount of mitochondria in the cell? and to import this data into this spreadsheet. I am have been searching my brains out through google, and I cant find any clever way to do this? Which codes and commands should I look into?