Community Profile

Peyman Obeidy

Centenary Institute of Cancer Medicine and Cell Biology

35 total contributions since 2016

Peyman Obeidy, PhD
Research Officer in Immune Imaging program at
Centenary Institute of Cancer Medicine and Cell Biology

Associated with Sydney Medical School, University of Sydney

Interested in: quantitative image analysis for single molecule, live cell, and fixed tissue

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Question

voronoin option for only selecting bound cells in voronoi graph
Hi all, I am trying to find all the neighbor of each Voronoi cell using <https://people.sc.fsu.edu/~jburkardt/m_src/voronoi_...

2 years ago | 0 answers | 0

0

Question

Find unique rows (including rows with reverse x,y) in matrix of x,y coordinates
Hi, I would appreciate your comments on this problem. I would like to extract unique coordinates for example if x=1, y=2, th...

2 years ago | 1 answer | 0

1

How can I get all the cells connected to each individual cells of a Voronoi diagram?

3 years ago | 0

| accepted

Question

How can I get all the cells connected to each individual cells of a Voronoi diagram?
How can I get all the cells connected to each individual cells of a Voronoi diagram? I need this to get access to each connec...

3 years ago | 2 answers | 0

2

Question

Adding a scatter of points to a boxplot
Does anyone come with with a code which can match the python generated boxplot?

3 years ago | 3 answers | 0

3

how to create a new folder mkdir, but naming that folder as input before running the code
not quite sure what you want to do, but try this clear clc path =[pwd '\']; stru =dir( fullfile(pat...

3 years ago | 0

How do you decide about ref image, when calculating SNR
Given the image is stimulate and have a uniform noise, I should be able to calculate the SNR by simply dividing the mean signal ...

3 years ago | 0

| accepted

Question

How do you decide about ref image, when calculating SNR
I have a simulated image where a row of peaks is located in the middle of the image. Attached is the code that I write to calcul...

3 years ago | 1 answer | 0

1

Change file names which meet certain criteria to a new name
Answered by Looky. see above. % code clear clc path =[pwd '\']; stru =dir( fullfile(path, '*.vsi') ); fi...

3 years ago | 0

| accepted

Question

Change file names which meet certain criteria to a new name
I need to change 80 file names, which meet certain criteria and copy it into a new folder. I listed the relationship between the...

3 years ago | 1 answer | 0

1

Question

How to read vsi image format into matlab
Any idea about how to read vsi image format into matlab and convert it into tif?

3 years ago | 2 answers | 0

2

Question

How to remove the pattern from microscopy scanned image
To remove the pattern fro the image I am using an averaging filter (see the code below). It helps with removing the background b...

3 years ago | 1 answer | 0

1

Question

Sat1=regionprops(MaskIm, {'Area', 'Eccentricity', 'EulerNumber', 'MajorAxisLength', 'MinorAxisLength', 'Orientation', 'Perimeter...

3 years ago | 1 answer | 0

1

Question

'rolling-ball background substraction' in matlab
Is there a reliable 'rolling-ball background subtraction' scripts for matlab?

3 years ago | 1 answer | 0

1

Question

convert Virtual Slide Images (VSI) to tiff
Is there an way to convert Virtual Slide Images (VSI) to tiff in matlab?

3 years ago | 1 answer | 0

1

Question

How to script this: returns all the x coordinates that distance between X and Y are bigger than r distant ?
I put together this, which is returning the y coordinates that are having greater distance than 2 e.g. % rng(1); % For re...

4 years ago | 1 answer | 0

1

Question

Find the distance between the longest endpoints of a skeleton
How to find the distance between the longest endpoints of a skeleton? LengthBr = bwmorph(finalBinaryImage,'skel',Inf); ...

4 years ago | 1 answer | 0

1

add an slider to get value for activecontour
The final code is provided here: https://au.mathworks.com/matlabcentral/answers/332877-update-image-in-gui-without-guide

4 years ago | 0

Question

update image in GUI without GUIDE
I am new to GUI without GUIDE, and I would appreciate any help in completing this function. I need it to get the value from the ...

4 years ago | 1 answer | 0

1

Question

add an slider to get value for activecontour
% Display segmented image BWsIbf = activecontour(ImCh1,BWCh1, 400, 'edge'); % FinalImwithMask=imfuse(BWsIbf,Im...

4 years ago | 1 answer | 0

1

Question

Semi-automatic cell segmentation to be converted to GUI
I find it difficult to find an algorithm that can always come up with a reasonable segmentation of cells in microscopy fluoresce...

4 years ago | 0 answers | 0

0

% while(1) %%your code here promptMessage = sprintf('Do you want to Continue processing,\nor Cancel to abort processing?');...

4 years ago | 0

Find the closest co-ordinates (between to uneven list of cooardinates)
Thank you both, I think knnsearch works better, as you see I have 13 points in PointinCh2, so I expect to find them in PointinCh...

4 years ago | 0

Question

Find the closest co-ordinates (between to uneven list of cooardinates)
I want to select the coordinates in PointinCh1 list which have a coordinates in PointinCh2 list close to them. The code that I a...

4 years ago | 3 answers | 0

3

find closest Coordinates to a point
I have multiple values for A, so what I did is as follows; PointinCh1 = 20 482 19 359 45 438 ...

4 years ago | 0

find closest Coordinates to a point
This is very helpful, thank you for sharing. A question, how do I get the indexes for B (I want the index of the value which...

4 years ago | 0

Saving outputs to different folder than m-file.
[fName, pName] = uigetfile('*.tif');

4 years ago | 0

Saving outputs to different folder than m-file.
Thank you, this will help you to create a new folder and save the outcome into the new folder % code %make a new direct...

4 years ago | 0