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Image Segmentation Tutorial ("BlobsDemo")

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27 Aug 2009 (Updated )

Image Processing Tutorial to demonstrate the basic concepts to beginner users.

Editor's Notes:

This file was selected as MATLAB Central Pick of the Week

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Description

Perfect for the beginner, this demo illustrates simple object detection (segmentation, feature extraction), measurement, and filtering. Requires the Image Processing Toolbox (IPT) because it demonstrates some functions supplied by that toolbox, plus it uses the "coins" demo image supplied with that toolbox. If you have the IPT (you can check by typing ver on the command line), you should be able to run this demo code simply by copying and pasting this code into a new editor window, and then clicking the green "run" triangle on the toolbar.

First finds all the objects, then filters results to pick out objects of certain sizes. The basic concepts of thresholding, labeling, and regionprops are demonstrated with a simple example.

It's a good tutorial for those users new to MATLAB's image processing capabilities to learn on, before they go on to more sophisticated algorithms.

Tested with R2008b through R2011b.

Acknowledgements

This file inspired Simple Color Detection By Hue.

Required Products Image Processing Toolbox
MATLAB release MATLAB 7.7 (R2008b)
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Comments and Ratings (103)
19 Nov 2014 Salaheddin Hosseinzadeh

Thanks a lot for sharing ;)

18 Oct 2014 Akash Ghode  
22 Sep 2014 Dakala Jayachandra  
20 Sep 2014 Durga g_C  
12 Sep 2014 Rushikesh Tade

Nice work!

11 Sep 2014 alex yang  
22 Apr 2014 Shien Kwun Leong

Dear Image Analyst,

Thank you for this beautiful code. I'm trying to use it for oil palm ripeness detection.

13 Apr 2014 ramin bba

Looks simple and sophisticated at the same time! Full of comments and as such easy to follow the chain of thoughts of the author. One can simply make adjustments based on his/her needs. Great job Image Analyst!

28 Mar 2014 fereshte

hi

i get an error...please help me.

??? Error using ==> cd
Cannot CD to (Name is nonexistent or not a directory).

26 Mar 2014 xsfeng

Dear Image Analyst,

Thanks for this beautiful code. I have a minor question concerning about the 'keeper' blob image. Is that possible that we segment the keeper blobs while still keep their numbers on it? Like tracing which number of blobs are the brightest and which number are the darkest? How should I write the code?

Thanks for your help!

24 Mar 2014 Yogesh Babu

Hello,
I used this code to find the Area of the each object this file does,But I am in need of number occurrence of same object should be known and that should be plotted..

24 Feb 2014 Scott

Works perfectly - very helpful!!

29 Dec 2013 Onesmo  
25 Dec 2013 Explorer

I also got the same errors as xsfeng when I run it.

Error using fileparts
Too many output arguments.

Error in BlobsDemo (line 191)
[thisFolder, baseFileName, ext, version] = fileparts(thisFile);

14 Dec 2013 Lourdes

dghgfh

12 Dec 2013 raviraja  
04 Dec 2013 xsfeng

Dear Image Analyst,

I got the error information when I run this scripts:

Error using fileparts
Too many output arguments.

Error in BlobsDemo (line 191)
[thisFolder, baseFileName, ext, version] = fileparts(thisFile);

Could you please help me with this? Many thx!

02 Dec 2013 adan flores

ok good programing

23 Sep 2013 Image Analyst

mustafs, the more sophisticated algorithms are more dependent on image content. More complicated content requires more complicated algorithms. I did add some demos on color segmentation, but I want to stick to fairly standard kinds of segmentation since there are an infinite number of unique, peculiar ones.

23 Aug 2013 hilal  
21 Jul 2013 Mario Garcia  
19 Jul 2013 mangood UK

dear image analyst,
can you please make to us more advance segmentation algorithms for different industrial application
the segmentation process is the most hard operation for all

19 Jul 2013 Valeska Pearson  
19 Jul 2013 Valeska Pearson

Hello image analyst,

How did you obtain the values to divide between foreground and background, at your thresholding code.

for example, why 70 and 0.94
thresholdValue - 70), double(0.94 * maxYValue(2))

24 May 2013 Jean Bilheux

Looking at the code taught me a few new tricks ...very nice.

12 May 2013 Chethan

Awesome, a nice presentation on feature extraction.

06 May 2013 Arul  
12 Apr 2013 Charles

This is so helpful. Thank you so much!

02 Mar 2013 brahim ouali

Excellent!!!

16 Feb 2013 vo danh  
16 Feb 2013 MOHD  
15 Feb 2013 Image Analyst

Nina, to do that exactly, you'd need to use John D'Errico's interparc program. Look for it in the File Exchange. You can also subsample, like thisBoundary(1:10:end,2) though these won't necessarily be evenly spaced in distance.

08 Feb 2013 Nina

Very useful demo. I do have a question Image Analyst - I hope you see this! For the part of the code:

boundaries = bwboundaries(binaryImage);
numberOfBoundaries = size(boundaries);
for k = 1 : numberOfBoundaries
thisBoundary = boundaries{k};
plot(thisBoundary(:,2), thisBoundary(:,1), 'g', 'LineWidth', 2);
end
hold off;

Is it possible to plot say only 10 points equally spaced around the boundary? Are they in order say clockwise or anticlockwise?

06 Jan 2013 Richi

Very nice, saved me at least one day!

06 Jan 2013 mustafa alnasser  
12 Nov 2012 Nad

is the actual tutorial available to watch online? cannot seem to locate it.

21 Oct 2012 Image Analyst

If anyone has any questions about their own specific images, they should ask in the Answers forum (look at the menu above). Do not put your specific question here as a comment on this program. I can help there in Answers. This page is not meant to be a discussion forum.

19 Oct 2012 microF

Hello Image Analyst ,

your demo is excatly what I am looking for to analyse my fluorescence images. However my images are taken with a 12 bit peltier cooled fluorescence camera and saved as .tif. I can hence not display their histograms without getting an error:
" Warning: Image is too big to fit on screen; displaying at 67% "

I tried to plot the histogram using

plot_size = get(0,'ScreenSize');
fg1 = figure(1);
set(fg8, 'Color', [1 1 1], 'Position', plot_size, 'Visible', 'on');
[pixelCount grayLevels] = imhist(orginalimage);
bar(pixelCount); title('Histogram of orginalimage');
xlim([0 grayLevels(end)]);

but it didnt help. I would really appreciate any help and comments.

Cheers
microF

21 Sep 2012 abhinav gupta

Hey this demo has been very useful.....my project is wavelength calculation using diffraction grating, so we get an image which will be a series of round dots and we should find the distance between two successive points.......so with this blob i can find the dots but how to find the centres of those dots?????? plz help me anyone... i would be greatful......ty in advance

21 Sep 2012 Steven

Thanks for showing us a basic demo. It helped a lot!

11 Sep 2012 MML

thanks for sharing this demo. This provides a very good example for beginners.

11 Sep 2012 MML  
22 Aug 2012 Image Analyst

Christie, when you adapted it, you had it read in a color image, even if it doesn't look like it. Do this to prove: [rows columns NumberOfColorChannels] = size(yourImage). Use rgb2gray() right after you call imread() to convert your color image into a gray scale image.

24 Jul 2012 Christie

Hey, Image Analyst,

Sorry, I tried to send this as a message first but kept getting an error from the site. Anyway, I am using your BlobsDemo to find the area of leaf surfaces traced onto a piece of graph paper. The code has no problem translating it into a binary image with clearly defined leaves and no graph paper grid, but when it tries to label each blob I get the following error:

??? Error using ==> iptcheckinput
Function BWLABEL expected its first input, BW, to
be two-dimensional.

Error in ==> bwlabel at 67
iptcheckinput(BW, {'logical' 'numeric'}, {'real',
'2d', 'nonsparse'}, ...

Error in ==> LeafArea at 48
labeledImage = bwlabel(binaryImage, 8); % Label
each blob so we can make measurements of it

What does it mean when it says the image isn't 2-dimensional?

Thanks for your help,

Christie

02 Jun 2012 khalid  
30 May 2012 Aliyu Abdu

I'm finding your Demo quite very useful in my work. Thank you.

31 Mar 2012 zaidan

it's nice info for beginner thank's

22 Feb 2012 Ryan  
19 Feb 2012 Tulips  
20 Jan 2012 Image Analyst

Syahrul, it does do segmentation into several areas - each coin is a different area. How can you label something without having a binary image? You can't, but why would you want to avoid labeling even if you could?

20 Jan 2012 Image Analyst

sivan, you must have a color image for some reason. You probably changed the filename to one of your images. Coins.png that my demo uses is a monochrome (gray scale) image.

19 Jan 2012 Syahrul Niezam

is it possible to do segmentation into several areas, not binarization before labeling?

06 Dec 2011 Fer  
05 Nov 2011 Image Analyst

If anyone wants to ask me a question, click my name above, then click the "Contact Author" link.

24 Aug 2011 Nicolas  
13 Aug 2011 sivan saminathen

can any wan help me...why i got error in the code when i try to run it..in line 41-[pixelCount grayLevels] = imhist(originalImage);...this code..the error said

("??? Error using ==> iptcheckinput
Function IMHIST expected its first input, I or X, to be two-dimensional.")

why it said so...i just keep on follow the code given but suddenly it give error

22 Jul 2011 Lim

Hi I appreciate this demo very much. I modify your code to work along with watershed segmentation for my image (blood cell), and it turns out good. However, how do I filter the background after I plot the boundaries of the selected cell? (so that the resulting image only shows the blobs without the background) The cropping works very well too but I don't want to involve the background. Thank you.

05 Jun 2011 Image Analyst

German:
You ask this kind of question on the newsgroup or on Answers, not as a comment on people's File Exchange submissions. I'd be happy to answer it there.

24 May 2011 German Espinal

Please I need some help !!! I need to capture a basic color card with my webcam, then I need to determine what color is it. Matlab code analize and gives the answer. Example: The card is yellow. Can someone of you Help me please with the MatLab code ???? TKS A lot !!!

22 May 2011 German Espinal

Hi guys !!! I need to capture a primary color card with my webcam, then I need to determine what color is it ??? Can someone of you Help me please with the MatLab code ???? TKS A lot !!!

10 May 2011 K

Thanks!

10 May 2011 K

I should read code comments more thoroughly. No need to answer. Thanks!

24 Apr 2011 akbarul

thank you

10 Mar 2011 Jason  
01 Mar 2011 Pierre

Please can somebody send me the matlab code for gray scale image segmentation plzzzz...?I will be very greatful

01 Mar 2011 shantha

Hello!

I'm pretty new to matlab.Can you offer some help regarding my issue?
I need a code to extract objects from a single image and write the extracted objects to separate images.As an example if an image consists of say an elephant and tree , I want to extract these two objects and write as separate images..

22 Feb 2011 Nicolas

Very cool code.

21 Feb 2011 Nicolas  
05 Feb 2011 Image Analyst

Manhal, I used Photoshop to create an image with 12 coins and it worked just fine. You must have done something wrong.

05 Feb 2011 Image Analyst

Vivek, what is it about this that made you think it was a 1 star? Is there anything I could improve with it to help beginners understand it better?

12 Jan 2011 Manhal

and one more thing, I tried to change the image that is used in the BlobsDemo, by adding 2 more coins, but still show that we already have 10 objects...
is there something should I change to make it works??

03 Dec 2010 Naresh Pai

Useful and well-commented code that demonstrates image thresholding. Connected components, including real world objects, in an image is of interest to many and this code provides the starting point for such projects. Thanks IA.

12 Nov 2010 Anthony

An excellent demonstration of simple image segmentation. Also a nice introduction to the image toolbox in Matlab. The functions for dealing with connected components (centroid, mean, etc) should be extremely useful.

02 Nov 2010 Vivek Maik  
15 Oct 2010 Image Analyst

J.D, you need to get some model of skin color. I know that it's a boomerang- or banana-shaped cluster in HSV color space. You need to define parameters to model that, and then segment it, possibly with a 3D lookup table instead of a mathematical model, or with the mathematical model if you can come up with the formulas. But I know you can't simply do high and low thresholding in any color space to carve out a box that selects the skin color pixels.

24 Sep 2010 J.D

hello ~ i juz want to ask you what should i do if i want to recognize color of human skin~ i want to get its hsv value for every pixel of the human face ~ and then exlude the eye and mouth part~ i want to get the value as my input to train in neural network~ can u help me~ urgent.. tq~

22 Sep 2010 Image Analyst

Christopher. Yes there are lots of more complicated images that could be used that would be more challenging. I work with many of those kinds of images. However I know from my newsgroup postings that even code as simple as this blows a lot of people away. So thanks for the suggestion but I think I'll keep it simple. I do have some color demos posted that are slightly more challenging.

15 Aug 2010 Walaa Gouda

Hi I am working in my master about breast cancer mass detection the first step is to determine region of interest which is the breast contour and i need help in this step as i don't know how to do this so please if there is anyone who can help me
thanks

01 Jul 2010 trypsin

i am just trying it

01 Jul 2010 Christopher

Interesting demonstration ImageAnalyst. Fortunately the 'coins' sample image has high contrasting content which allows for easy selection of the threshold. Plus the coins allow for the 'imfill' operation to perform the majority of the work.

It would be interesting to see results on an image with a much smoother histogram but this is where image segmentation gets complicated I guess...

All in all, a nice demonstration of the capabilities that both the IPT and Mathematical Morphology can provide in image processing applications.

01 Jul 2010 Nitin  
06 Jun 2010 Ben

hello every body, can you give me a code for building extraction using mathematical morphologie ?? and thanks a lot

17 May 2010 Farie

Hi, I've tried your demo but it's not working for 3D images. Is there any way to solve this problem? Thanks

14 Apr 2010 aravind prajan  
25 Mar 2010 Image Analyst

Like other submissions that are meant to demonstrate certain toolboxes, you need to have the toolbox. If you don't have it, you can buy it, or write the necessary toolbox functions yourself. Generally they are the functions starting with the letters "im" or "bw".

25 Mar 2010 John Brathwaite

What if I don't have the IPT??

12 Mar 2010 David JL

I just realized I use Matalb R2007b, not R2008. I guess that is the problem. Sorry about that.

09 Mar 2010 Kris

Very useful...great work...

12 Feb 2010 Yuvaraj

great work..I have one question for U. using my web cam i will capture a picture which will contain a ball in a room. now how can i separate the ball (circular shaped) from the background and i want to find the area of that ball(circle). how can i edit your code for this particular task.

07 Feb 2010 Nitin  
05 Feb 2010 Image Analyst

Jimmy - ask in the newsgroup. Let's take this conversation there.

30 Jan 2010 Jimmy

Ok let's forget about GUI, I am not even sure if I need to use it. The reason I asked if I can get more than one image read is than after I modified the code I got my the centroids of all objects in the images. The results are in vector form [x y]. For example
[29 134]. I want to make a loop going through all images and objects in them, reading those measurements. Can you give me an advice? Thank you

28 Jan 2010 Husam Aldahiyat

Excellent!!!

27 Jan 2010 Image Analyst

Jimmy, just paste whatever code you want into line 1076 of that app after you've deleted lines 1076-1164. Then just run it with the green triangle. You need all the rest of the code because that is the GUI. To select images, you simply click on their names in the listbox like you'd do with any app. No code is needed from you to handle clicking on a listbox - that's already done for you. Just click on the images you want to process and click the analyze button and it will analyze only those that you've clicked on.

25 Jan 2010 Jimmy

Ok I did as you said Image Analyst.I got some errors. Now do I only use 1076 - 1164 code or the whole Magic code which is huge? And another thing how do I select images from a folder? Do I need to put that into the code? Thank you

24 Jan 2010 Image Analyst

Jimmy, just follow these easy step by step instructions.
1. Open both his MAGIC code and my BlobsDemo code in MATLAB.
2. Copy all of my BlobsDemo code into the clipboard.
3. Go to AnalyzeSingleImage in his code, currently line 1075, and simply delete all of that function, which means delete lines 1076 - 1164. This is just like it says to do in the comments on line 1070 and 1071 of his code.
4. Now simply paste in my BlobsDemo code.
Now it should work. Adapt my/your code in that function as you see fit.

23 Jan 2010 Jimmy

Thank you for your reply Image Analyst. Yes, I know that I need to make changes according to the pictures regarding threshold etc.. What I don't understand is how to plug that code into AnalyzeSingleImage(). Is it possible for you to send me the example on testbest1@yahoo.com. Thank you

22 Jan 2010 Image Analyst

Jimmy, sure - just copy the code into your own program. One way to do it might be to use this in conjunction with MAGIC (http://www.mathworks.com/matlabcentral/fileexchange/24224) which does batch processing. Just take this code and plug it into his AnalyzeSingleImage() function. Then you'll be able to select several images from your folder, and process them. Of course, my code has several things that are special for the coins image and you'd have to modify several things for your images, such as the thresholds, etc.

17 Jan 2010 Jimmy

Great Work Image Analyst, very useful indeed. I want to ask one question: is there any chance that it can be applied to more than one image simultaniously? And if there is how can it be done. Thank you

05 Dec 2009 Image Analyst

Thomas, this is not an error in my code. sprint() is not a function - ParseInputs() should have called sprintf() instead. regionprops() and ParseInputs() are Mathworks code, not mine. I searched the R2008b version of ParseInputs and it no longer has sprint() in it, so they've fixed that bug.

Sorry that I can't test this with every prior version of MATLAB. I know it definitely works with R2008a and later. Since you are several years behind I suggest you get the most modern version of MATLAB.

29 Nov 2009 ThomasKUL Knaepen

Not working for me:

Running BlobsDemo.m...
??? Undefined command/function 'sprint'.

Error in ==> regionprops>ParseInputs at 878
msg = sprint('This measurement is not a string: "%d".', list{k});

Error in ==> regionprops at 114
[L, requestedStats] = ParseInputs(officialStats, varargin{:});

29 Nov 2009 ThomasKUL Knaepen

I got :

MATLAB Version 7.1.0.246 (R14) Service Pack 3
and the IPT

29 Aug 2009 us

an excellent and exceptionally well commented image processing demo by a seasoned ML user and senior CSSM citizen...

a few changes i'd make:
- put it into a function
-> no need for the bad CLEAR ALL...
- make the figure size smaller -and-
- put an ECHO ON/OFF at the beginning/end of the demo
-> for users to be able to enjoy the comments during run-time...

just a few thoughts
us

Updates
25 Mar 2010

Added label numbers to each blob. Extracted each blob to a separate image.

26 Mar 2010

Updated description and made change to how labeled image is displayed.

10 Apr 2010

Spelling correction in the description.

16 Mar 2012

Renamed main title and altered description slightly.

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