I need some help on spreadsheets in Matlab

Question

August Hoel 2018-10-25

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/426094-i-need-some-help-on-spreadsheets-in-matlab

评论： August Hoel 2018-10-26

在 MATLAB Online 中打开

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

6 个评论
显示 4更早的评论隐藏 4更早的评论

Guillaume 2018-10-26

在 MATLAB Online 中打开

Capture.PNG

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 2018-10-26

在 MATLAB Online 中打开

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        xxx        yyyy          zzzz        ccccc
            1        xxx        yyyy          zzzz        ccccc
            1        xxx        yyyy          zzzz        ccccc
            2        xxx        yyyy          zzzz        ccccc
            2        xxx        yyyy          zzzz        ccccc
            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 2018-10-26

在 MATLAB Online 中打开

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?

请先登录，再进行评论。

请先登录，再回答此问题。

I need some help on spreadsheets in Matlab

6 个评论
显示 4更早的评论隐藏 4更早的评论

回答（0 个）

另请参阅

类别

标签

产品

版本

Community Treasure Hunt

I need some help on spreadsheets in Matlab

6 个评论 显示 4更早的评论隐藏 4更早的评论

回答（0 个）

另请参阅

类别

标签

产品

版本

Community Treasure Hunt

6 个评论
显示 4更早的评论隐藏 4更早的评论