advice on counting objects

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Xinyu Zhao-2 Xinyu Zhao-2
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advice on counting objects

Search the CONFOCAL archive at
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Dear listers,

 I was wondering if anybody could give me some advice on how to count the
objects in the image as attached.  They were cross sections of inner segments
of rods and the goal is to get the total number of them.

It seemed a easy job at the beginning.  But after I started, I realizee that it
is tricky.  The intensity variation of the objects is big and the boundaries of
the cells are not clear.  

I am not much of an image processing person.  I was wondering if anybody could
give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104

#1978, ODA, 1,000um from ONH, 40X.tif (2M) Download Attachment
Glen MacDonald-2 Glen MacDonald-2
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Re: advice on counting objects

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Are you using confocal or widefield, was that image a single plane or  
a brightest point projection? what is the label and mountant?

Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
[hidden email]

************************************************************************
******
The box said "Requires WindowsXP or better", so I bought a Macintosh.
************************************************************************
******


On Feb 6, 2008, at 12:28 PM, Xinyu Zhao wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
> Dear listers,
>
>  I was wondering if anybody could give me some advice on how to  
> count the
> objects in the image as attached.  They were cross sections of  
> inner segments
> of rods and the goal is to get the total number of them.
>
> It seemed a easy job at the beginning.  But after I started, I  
> realizee that it
> is tricky.  The intensity variation of the objects is big and the  
> boundaries of
> the cells are not clear.
>
> I am not much of an image processing person.  I was wondering if  
> anybody could
> give me some advice on how to proceed.
>
> Thank you very much.
>
> Xinyu Zhao
> Biomedical Imaging Core Lab
> B110 Richards Building
> School of Medicine
> University of Pennsylvania
> 37th and Spruce Street
> Philadelphia, PA 19104<#1978, ODA, 1,000um from ONH, 40X.tif>
heckman@bgnet.bgsu.edu heckman@bgnet.bgsu.edu
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

  Zhao-
The first thing to explore would be the "edge" filter or kernel.  If
you have any software, such as Image ProPlus, MetaMorph, etc. (don't
mean to leave anyone out), it would probably let you execute this
function and see if you then have sharp boundaries.  There is
probably a plug-in for ImageJ as well, which maybe someone can point
out where it can be found.  (I couldn't really see your image, as my
computer treated it as a document.)
C.

>          Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
>Dear listers,
>
>  I was wondering if anybody could give me some advice on how to count the
>objects in the image as attached.  They were cross sections of inner segments
>of rods and the goal is to get the total number of them.
>
>It seemed a easy job at the beginning.  But after I started, I
>realizee that it
>is tricky.  The intensity variation of the objects is big and the
>boundaries of
>the cells are not clear.
>
>I am not much of an image processing person.  I was wondering if anybody could
>give me some advice on how to proceed.
>
>Thank you very much.
>
>Xinyu Zhao
>Biomedical Imaging Core Lab
>B110 Richards Building
>School of Medicine
>University of Pennsylvania
>37th and Spruce Street
>Philadelphia, PA 19104
>
>Attachment converted: Macintosh HD:#1978, ODA, 1,000um f#90B94.tif
>(TEXT/ttxt) (00090B94)


--
Carol A. Heckman, Ph.D.
Director, Center for Microscopy & Microanalysis
and Professor of Biological Sciences
Bowling Green State University
Bowling Green, OH 43403
USA
website: http://www.bgsu.edu/departments/biology/facilities/MnM
Deanne Veronica Catmull Deanne Veronica Catmull
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Xinyu,

I am no expert myself although I have just been to an imaging workshop
where they had a couple of talks which discussed image analysis for
counting and I know one in particular used a particular algorithm for
discriminating the edges of the cells or particles of interest.
You may want to try emailing the speaker Jean-Christophe Olivio-Marin
from the Pasteur Institute in Paris. What is your email address, I will
pass it on to you?

Kind regards,

Deanne.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Xinyu Zhao
Sent: Thursday, February 07, 2008 7:29 AM
To: [hidden email]
Subject: advice on counting objects

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal



Dear listers,

 I was wondering if anybody could give me some advice on how to count
the
objects in the image as attached.  They were cross sections of inner
segments
of rods and the goal is to get the total number of them.

It seemed a easy job at the beginning.  But after I started, I realizee
that it
is tricky.  The intensity variation of the objects is big and the
boundaries of
the cells are not clear.  

I am not much of an image processing person.  I was wondering if anybody
could
give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104
Julio Vazquez Julio Vazquez
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Xinyu, 

First, I think you will make your analysis easier and improve your counts by (a) using a confocal (or deconvolution), and/or (b) starting with a more even illumination field (by adjusting your scope fluorescence illumination, or taking a reference image and using it to perform background correction.  The dynamic range/contrast of the image seems quite low... maybe you could try to improve that too (better lens...?  use camera binning... ?)


Then, here's a quick and dirty method using imagej  ( http://rsb.info.nih.gov/ij/ ):


0. Open your image

1. Process > Subtract background (radius = 50) (flattens background)

2. Filter > Median (radius 2) (smoothes image)

3. Threshold (30-255), Apply (select thresholded pixels foreground color, remaining pixels background color, black foreground/white background) (thresholds image; play around to see which values work best for your image)

4. Process > Binary >Watershed (separates clusters... to some extent)

5. Go to Analyze > Set measurements and define the parameters to measure. If you just want a count, you may uncheck everything.  I recommend checking "Area" and "Display Label" Redirect: None

6. Analyze > Analyze particles; Check all boxes, and select Show outlines

7. Copy data to Excel. From the table of results, you can list particles by size, and you may be able to tell which of those are clusters (just measure the average size of a cell and do a ratio).


An even quicker and dirtier way is to measure carefully the surface area of a sample of well-separated cells (as shown above; just pick a good region and get the numbers for the cells that are well separated), threshold all the cells, get total positive area (Using Analyse > Measure, or using the summary with the method above), and divide by average cell area to get a count.

Not perfect, but it's a start. You can also look for more sophisticated segmentation plugins at the imagej web site.


--
Julio Vazquez
Fred Hutchinson Cancer Research Center
Seattle, WA 98109-1024



On Feb 6, 2008, at 12:28 PM, Xinyu Zhao wrote:

Search the CONFOCAL archive at



Dear listers,

 I was wondering if anybody could give me some advice on how to count the 
objects in the image as attached.  They were cross sections of inner segments 
of rods and the goal is to get the total number of them. 

It seemed a easy job at the beginning.  But after I started, I realizee that it 
is tricky.  The intensity variation of the objects is big and the boundaries of 
the cells are not clear.  

I am not much of an image processing person.  I was wondering if anybody could 
give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104<#1978, ODA, 1,000um from ONH, 40X.tif>

Xinyu Zhao-2 Xinyu Zhao-2
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Re: advice on counting objects

In reply to this post by Glen MacDonald-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi, Glen,

The picture is from one of our users.  It was taken somewhere else in the past
and the user would like to do the counting in our lab at this stage.  I have
no knowledge about the lablel and mountant.  But I believe widefield was used
and it was a single plane image, and the tissue was dog retina, likely whole
mount.  The objects here are cross-section view of the inner segments of the
rod cells.  Obviously it was not a good quality picture to start with, but
this is all he has got.  

Thank you very much for your attention.

Xinyu



Quoting Glen MacDonald <[hidden email]>:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Are you using confocal or widefield, was that image a single plane or  
> a brightest point projection? what is the label and mountant?
>
> Glen
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> Box 357923
> University of Washington
> Seattle, WA 98195-7923  USA
> (206) 616-4156
> [hidden email]
>
> ************************************************************************
> ******
> The box said "Requires WindowsXP or better", so I bought a Macintosh.
> ************************************************************************
> ******
>
>
> On Feb 6, 2008, at 12:28 PM, Xinyu Zhao wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> >
> >
> > Dear listers,
> >
> >  I was wondering if anybody could give me some advice on how to  
> > count the
> > objects in the image as attached.  They were cross sections of  
> > inner segments
> > of rods and the goal is to get the total number of them.
> >
> > It seemed a easy job at the beginning.  But after I started, I  
> > realizee that it
> > is tricky.  The intensity variation of the objects is big and the  
> > boundaries of
> > the cells are not clear.
> >
> > I am not much of an image processing person.  I was wondering if  
> > anybody could
> > give me some advice on how to proceed.
> >
> > Thank you very much.
> >
> > Xinyu Zhao
> > Biomedical Imaging Core Lab
> > B110 Richards Building
> > School of Medicine
> > University of Pennsylvania
> > 37th and Spruce Street
> > Philadelphia, PA 19104<#1978, ODA, 1,000um from ONH, 40X.tif>
>
>


--
Marius Messerli Marius Messerli
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

- commercial response -

Dear  Xinyu,

Imaris determined a count of 1859.

The procedure:
- drop image file into Imaris
- create new spot component
- step through detection wizzard
- open statistics

The Imaris Spot detection/analysis component knows how to handle variable
image intensity and cell size.

Let me know if you are interested in the final image (overlay of your
original image with detected spots) or an evaluation copy of Imaris.

Regards,
Marius

Marius MESSERLI, Ph.D.
CEO Bitplane
http://www.bitplane.com

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Xinyu Zhao
Sent: Mittwoch, 6. Februar 2008 21:29
To: [hidden email]
Subject: advice on counting objects

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal



Dear listers,

 I was wondering if anybody could give me some advice on how to count the
objects in the image as attached.  They were cross sections of inner
segments of rods and the goal is to get the total number of them.

It seemed a easy job at the beginning.  But after I started, I realizee that
it is tricky.  The intensity variation of the objects is big and the
boundaries of the cells are not clear.  

I am not much of an image processing person.  I was wondering if anybody
could give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104
Nuno Moreno Nuno Moreno
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Re: advice on counting objects- Course Annoucement

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi,

I was not intending to make it international but feel free to show up.
_______________________________________________________________________
The Cell Imaging and BioInformatics Units are organizing a course about
Quantitative image processing. It will be held at the IGC on the
bioiformatics computer room in 26 and 27 February.

Synopsis:
Imaging analysis, though very powerful, its also a subject of several
artifacts which have to be taken in account on experimental design and
acquisition. Notwithstanding, it is the desirable method for taking
information in microscopy, making us focus on the need of this approach,
acquisition details and results obtained within this scope. Because it
will be "problem oriented", applicants should propose a real or putative
problem for the practicals, which will be the most important selection
factor.

Instructors:
Nuno Moreno (Cell Imaging Unit-IGC) Course Organizer
José Leal (BioInformatics Unit-IGC)
Mónica Dias (Cell Cycle Regulation-IGC)
Gabriel Martins (Centro de Biologia Ambiental-FCUL)


For applying please visit:
http://bioinformatics.igc.gulbenkian.pt/events/39/

This course is restricted to 20 people and its free for IGC/ITQB
members, having a symbolic fee of 100 Euros for others.


See you there,
Nuno Moreno

Marius Messerli wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> - commercial response -
>
> Dear  Xinyu,
>
> Imaris determined a count of 1859.
>
> The procedure:
> - drop image file into Imaris
> - create new spot component
> - step through detection wizzard
> - open statistics
>
> The Imaris Spot detection/analysis component knows how to handle variable
> image intensity and cell size.
>
> Let me know if you are interested in the final image (overlay of your
> original image with detected spots) or an evaluation copy of Imaris.
>
> Regards,
> Marius
>
> Marius MESSERLI, Ph.D.
> CEO Bitplane
> http://www.bitplane.com
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On
> Behalf Of Xinyu Zhao
> Sent: Mittwoch, 6. Februar 2008 21:29
> To: [hidden email]
> Subject: advice on counting objects
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
> Dear listers,
>
>  I was wondering if anybody could give me some advice on how to count the
> objects in the image as attached.  They were cross sections of inner
> segments of rods and the goal is to get the total number of them.
>
> It seemed a easy job at the beginning.  But after I started, I realizee that
> it is tricky.  The intensity variation of the objects is big and the
> boundaries of the cells are not clear.  
>
> I am not much of an image processing person.  I was wondering if anybody
> could give me some advice on how to proceed.
>
> Thank you very much.
>
> Xinyu Zhao
> Biomedical Imaging Core Lab
> B110 Richards Building
> School of Medicine
> University of Pennsylvania
> 37th and Spruce Street
> Philadelphia, PA 19104
>

--
Nuno Moreno
Cell Imaging Unit
Instituto Gulbenkian de Ciência
http://uic.igc.gulbekian.pt
http://www.igc.gulbekian.pt
phone +351 214464606
fax   +351 214407970
Winnok H. De Vos Winnok H. De Vos
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Re: advice on counting objects

In reply to this post by Julio Vazquez
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi,

An alternative simplistic approach that might do relatively well for rough numbers ,would be something like:

 

(first open your image)

//setBatchMode(true);

title=getTitle();

run("Pseudo Flat Field", "mean=100 32-bit");rename("Flat");

run("Gaussian Blur...", "sigma=3");rename("Blur");

setAutoThreshold();

run("Find Maxima...", "noise=0 output=[Segmented Particles] exclude above");

selectWindow("Blur");close();

rename("particles");run("Invert");

run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Outlines display exclude clear record");

selectWindow("particles");close();

selectWindow("Drawing of particles");rename("outlines");

run("Invert");

run("RGB Merge...", "red=outlines green=["+title+"] blue=*None* gray=*None*");

rename("output");

//setBatchMode("exit and display");

 

As you can see it is still is prone to include some errors, due to smoothing, especially at the edges, because they are blurred (no plan lens?). You might want to consider clipping of the edges , e.g., by selecting a rectangular ROI for analysis.

Kind regards,Winnok

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Julio Vazquez
Sent: donderdag 7 februari 2008 1:12
To: [hidden email]
Subject: Re: advice on counting objects

 

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Xinyu, 

 

First, I think you will make your analysis easier and improve your counts by (a) using a confocal (or deconvolution), and/or (b) starting with a more even illumination field (by adjusting your scope fluorescence illumination, or taking a reference image and using it to perform background correction.  The dynamic range/contrast of the image seems quite low... maybe you could try to improve that too (better lens...?  use camera binning... ?)

 

 

Then, here's a quick and dirty method using imagej  ( http://rsb.info.nih.gov/ij/ ):

 

 

0. Open your image

 

1. Process > Subtract background (radius = 50) (flattens background)

 

2. Filter > Median (radius 2) (smoothes image)

 

3. Threshold (30-255), Apply (select thresholded pixels foreground color, remaining pixels background color, black foreground/white background) (thresholds image; play around to see which values work best for your image)

 

4. Process > Binary >Watershed (separates clusters... to some extent)

 

5. Go to Analyze > Set measurements and define the parameters to measure. If you just want a count, you may uncheck everything.  I recommend checking "Area" and "Display Label" Redirect: None

 

6. Analyze > Analyze particles; Check all boxes, and select Show outlines

 

7. Copy data to Excel. From the table of results, you can list particles by size, and you may be able to tell which of those are clusters (just measure the average size of a cell and do a ratio).

 

 

An even quicker and dirtier way is to measure carefully the surface area of a sample of well-separated cells (as shown above; just pick a good region and get the numbers for the cells that are well separated), threshold all the cells, get total positive area (Using Analyse > Measure, or using the summary with the method above), and divide by average cell area to get a count.

 

Not perfect, but it's a start. You can also look for more sophisticated segmentation plugins at the imagej web site.

 

 

--

Julio Vazquez

Fred Hutchinson Cancer Research Center

Seattle, WA 98109-1024

 

 

 

On Feb 6, 2008, at 12:28 PM, Xinyu Zhao wrote:



Search the CONFOCAL archive at

 

 

 

Dear listers,

 

 I was wondering if anybody could give me some advice on how to count the 

objects in the image as attached.  They were cross sections of inner segments 

of rods and the goal is to get the total number of them. 

 

It seemed a easy job at the beginning.  But after I started, I realizee that it 

is tricky.  The intensity variation of the objects is big and the boundaries of 

the cells are not clear.  

 

I am not much of an image processing person.  I was wondering if anybody could 

give me some advice on how to proceed.

 

Thank you very much.

 

Xinyu Zhao

Biomedical Imaging Core Lab

B110 Richards Building

School of Medicine

University of Pennsylvania

37th and Spruce Street

Philadelphia, PA 19104<#1978, ODA, 1,000um from ONH, 40X.tif>

 

 

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Checked by AVG Free Edition.
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David Barnes-2 David Barnes-2
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
On Jan. 23rd, there was a webinar on counting and tracking. The invitation was posted to this list. It is archived at
On Feb 6, 2008 3:28 PM, Xinyu Zhao <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal



Dear listers,

 I was wondering if anybody could give me some advice on how to count the
objects in the image as attached.  They were cross sections of inner segments
of rods and the goal is to get the total number of them.

It seemed a easy job at the beginning.  But after I started, I realizee that it
is tricky.  The intensity variation of the objects is big and the boundaries of
the cells are not clear.

I am not much of an image processing person.  I was wondering if anybody could
give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104

Paul Jantzen Paul Jantzen
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

**Commercial response - Image-Pro Plus method (but would apply to any other
software which has these tools)**

This image does indeed have a highly variable background, however this can
be overcome using a couple of simple tools in Image-Pro Plus from Media
Cybernetics (and other places, but this is my comfort zone :) ), the
procedure would be:

1) Convert image class to GS8 (this is an 8-bit palette image);
2) Run a Local Max filter on the image (I used a 21x21x1 kernel as this is a
2D image, single pass);
3) Dilate 7x7 (connects local max regions within objects);
4) Use the Count/Size module to count all independent objects, setting clean
borders to ALL (to not risk double counting objects).

I get a result on this image of 1892 objects.  An overlay of the processed
image with the original showing nice correlation between processed counted
bits and the original data can be found here:
ftp://ftp.mediacy.com/uploaded/Xinyu/CountOverlay.jpg (258Kb thus not
attached - if you want it directly please ask offline).  There are some
potential false positives in background regions, so I could tweak the filter
settings a bit, but I prefer to leave that as an exercise for the end user.  

If you want more information or a trial of the software, please let me know.

Cheers,
Paul Jantzen
Product Manager, Analytical Software Products
Media Cybernetics, Inc.
Weis, Michael Weis, Michael
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I have used Imaris exclusively for the visuaization of our 3D Confocal data sets. I followed your procedure for counting spots on this 2D image and was very impressed at the ease and quality of the spot counting even with the highly variable background. I am definitely going to use Imaris more on our 2D data. Thank you Marius!

Michael Weis
Electron Microscopy & Digital Imaging
Pacific Agri-Food Research Centre
Agriculture and Agri-Food Canada
4200 Highway 97
Summerland, BC  V0H 1Z0
Telephone: 250-494-6410
Facsimile: 250-494-0755
[hidden email]
 



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Marius Messerli
Sent: Thursday, February 07, 2008 12:46 AM
To: [hidden email]
Subject: Re: advice on counting objects


Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

- commercial response -

Dear  Xinyu,

Imaris determined a count of 1859.

The procedure:
- drop image file into Imaris
- create new spot component
- step through detection wizzard
- open statistics

The Imaris Spot detection/analysis component knows how to handle variable
image intensity and cell size.

Let me know if you are interested in the final image (overlay of your
original image with detected spots) or an evaluation copy of Imaris.

Regards,
Marius

Marius MESSERLI, Ph.D.
CEO Bitplane
http://www.bitplane.com

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Xinyu Zhao
Sent: Mittwoch, 6. Februar 2008 21:29
To: [hidden email]
Subject: advice on counting objects

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal



Dear listers,

 I was wondering if anybody could give me some advice on how to count the
objects in the image as attached.  They were cross sections of inner
segments of rods and the goal is to get the total number of them.

It seemed a easy job at the beginning.  But after I started, I realizee that
it is tricky.  The intensity variation of the objects is big and the
boundaries of the cells are not clear.  

I am not much of an image processing person.  I was wondering if anybody
could give me some advice on how to proceed.

Thank you very much.

Xinyu Zhao
Biomedical Imaging Core Lab
B110 Richards Building
School of Medicine
University of Pennsylvania
37th and Spruce Street
Philadelphia, PA 19104
JOEL B. SHEFFIELD JOEL B. SHEFFIELD
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Re: advice on counting objects

In reply to this post by Xinyu Zhao-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I'll throw one more possibility into the mix.  I used the ImageJ FFT
bandpass filter, set at a high value of 100, and a lower value of 0
to smooth out the background. --very impressive!.  I then set a
threshold, and ran a watershed algorithm. --ended up with about 1900
particles.  This seems higher than some have reported. I used a
cutoff of 10 pixels^2, and that may have included some small specks.  
 Perhaps it is worth comparing.

Joel

Date sent: Wed, 6 Feb 2008 15:28:52 -0500
Send reply to: Confocal Microscopy List
<[hidden email]>
From: Xinyu Zhao <[hidden email]>
Subject: advice on counting objects
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
> Dear listers,
>
>  I was wondering if anybody could give me some advice on how to count the
> objects in the image as attached.  They were cross sections of inner segments
> of rods and the goal is to get the total number of them.
>
> It seemed a easy job at the beginning.  But after I started, I realizee that it
> is tricky.  The intensity variation of the objects is big and the boundaries of
> the cells are not clear.  
>
> I am not much of an image processing person.  I was wondering if anybody could
> give me some advice on how to proceed.
>
> Thank you very much.
>
> Xinyu Zhao
> Biomedical Imaging Core Lab
> B110 Richards Building
> School of Medicine
> University of Pennsylvania
> 37th and Spruce Street
> Philadelphia, PA 19104
>


--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs
Zoltan Zoltan
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Re: advice on counting objects

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
 
 
I've got 1656 with similar method in ImageJ.  First used FFT, cutting out appr. 80% of the frequency spectrum, using four quadrants (one from each corner) and a small cut from the very centre, but leaving the local maxima corresponding to the periodic image elements.  The inverse FFT was then calculated and brightness and contrast improved and then thresholded.  The Particle Counting -> Nucleus Counter from Plugins was then used and seemed to work well, giving 1656. I'll run it through Volocity to separate touching objects tomorrow.
 
Zoltan 
 
 

 
On 2/7/08, Joel Sheffield <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I'll throw one more possibility into the mix.  I used the ImageJ FFT
bandpass filter, set at a high value of 100, and a lower value of 0
to smooth out the background. --very impressive!.  I then set a
threshold, and ran a watershed algorithm. --ended up with about 1900
particles.  This seems higher than some have reported. I used a
cutoff of 10 pixels^2, and that may have included some small specks.
Perhaps it is worth comparing.

Joel

Date sent:      Wed, 6 Feb 2008 15:28:52 -0500
Send reply to:  Confocal Microscopy List
<[hidden email]>
From:   Xinyu Zhao <[hidden email]>
Subject:        advice on counting objects
To:     [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
> Dear listers,
>
>  I was wondering if anybody could give me some advice on how to count the
> objects in the image as attached.  They were cross sections of inner segments
> of rods and the goal is to get the total number of them.
>
> It seemed a easy job at the beginning.  But after I started, I realizee that it
> is tricky.  The intensity variation of the objects is big and the boundaries of
> the cells are not clear.
>
> I am not much of an image processing person.  I was wondering if anybody could
> give me some advice on how to proceed.
>
> Thank you very much.
>
> Xinyu Zhao
> Biomedical Imaging Core Lab
> B110 Richards Building
> School of Medicine
> University of Pennsylvania
> 37th and Spruce Street
> Philadelphia, PA 19104
>


--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs



--
--
Zoltan Cseresnyes
Facility manager, Imaging Suite
Dept. of Zoology University of Cambridge
Downing Street, Cambridge
CB2 3EJ    UK

Tel.: (++44) (0)1223 769282
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