How do I run colonycount to count bacterial colonies?

I recently downloaded the latest version of Matlab; however, I have never used Matlab previously. I found out that Matlab is able to count the colonies of bacteria samples in a petri dish, but I do not know 1) where to find the already available program within Matlab, and 2) how to execute it once I have it available? Any help would be greatly appreciated. Thanks.

[Image Analyst]

How should it do this? From an image using image analysis? If so, post a picture. And you can check out my Image Segmentation Tutorial in my File Exchange.

[Jeremy Kunz]

Yes it analyzes an image to count the dots that are the colonies of bacteria. Please see attached image as an example. I have seen a youtube video https://www.youtube.com/watch?v=q3iCvrU8iBQ using Matlab to do this; however, it is an older version of Matlab and I am a new user so I am not familiar with Matlab and need step-by-step instructions. Thanks.

[John D'Errico]

Hmm. You stated in your question that you have downloaded the latest version of MATLAB. In your comment, you state that you have an older release. Only ONE of these statements can be true. Which is it?

[Jeremy Kunz]

Actually in my question I stated that I downloaded the latest version and in my comment and said, "I have seen a youtube video using Matlab" and the version used in the video is an older version so both my comment and my question are consistent and both are true. Did you see the link to the youtube video? Thanks.

Answer 1

[Walter Roberson]

http://www.mathworks.com/matlabcentral/fileexchange/35943-automated-counting-of-bacterial-colonies

http://www.mathworks.com/help/vision/examples/cell-counting.html

[Jeremy Kunz]

I did see the first link you posted, which appears to be what I am looking for. My problem is as a new user I do not know how to run that program. I get an error every time, including when I run his demo, and I am not sure if it is an issue with the program or if my lack of Matlab experience is the issue. I am looking for step-by-step instructions if possible. Thank you.

[Walter Roberson]

Telling us what the error message is saves us a lot of guessing.

Did you download http://www.mathworks.com/matlabcentral/fileexchange/26978-hough-transform-for-circles ?

[Jeremy Kunz]

Yes I did download the what was at that link. Below is what I entered with the error received. >>I='plate_example.jpg';

>> colony_count(I,115)

Undefined function or variable 'colony_count'.

[Walter Roberson]

Did you unzip the file into a directory and then use pathtool to add the directory to your MATLAB path?

[Image Analyst]

Maybe it expects the (poorly-named) I to be an image rather than a string. Try

myImage = imread('plate_example.jpg');
colony_count(myImage,115);

[Jeremy Kunz]

Yes I did unzip it and made sure it was in the MATLAB path. When I enter the above syntax I received the following error:

Error using vertcat Dimensions of matrices being concatenated are not consistent.

Error in circle_houghpeaks (line 109) peaks = [x'; y'; radii(rind)];

Error in colony_count (line 58) peaks = circle_houghpeaks(h, radii, 'npeaks', 10); % Pick top 10 circles.

[Walter Roberson]

You need to pass the image content rather than the name, and you need to pass a range of radii.

Answer 2

[sukumar thirugnanm]

??? Error: File: circle_houghpeaks.m Line: 113 Column: 11

Expression or statement is incorrect--possibly unbalanced (, {, or [.

Error in ==> colony_count at 58

peaks = circle_houghpeaks(h, radii, 'npeaks', 10); % Pick top 10 circles.

Error in ==> colony_count_demo at 15

[count,markers,mask] = colony_count(I,radii);

Anybody correct this code

Answer 3

[changsong]

I know an android app can do it named CountThings By Camera

you can download try it

download url https://play.google.com/store/apps/details?id=cn.movingshop.counting.global