Posted by
Daniel James White on
Jul 08, 2010; 3:45pm
URL: http://imagej.273.s1.nabble.com/Re-Automatic-Cell-Counting-tp3687675p3687676.html
Hi Francie,
these images are very nice....
but there is little chance that any simple method on the computer will be able to correctly segment
most of that DAPI nuclei in that image.
Even the other red channel is hard.
the objects overlap too much and there is no intensity max at their centre you could use.
THer tissue is very densly packed.
In this case you need something quite high tech,
where you can use a pipeline of methods to get the nuclei you want.
CellProfiler might be a good palce to start,
ir a macro or script in imageJ/Fiji
you need to find a local collaborator to help you out.
If you want to kist know the average brightness of the nuclei, that is possible my estimating the number
and measuring a few cells, then measuring the total intensity in the image.
what is it that you actually want to know from these images?
cheers
Dan
On Jul 7, 2010, at 7:17 PM, Barron, Francie wrote:
> Hi Dan,
>
> I converted to jpg, cut it in half on size. Hopefully this goes though.
>
> ~Francie
>
> NOTE NEW EMAIL ADDRESS:
[hidden email]
>
> ***************************************************************
>
> Francie Barron (Hyndman), Graduate Student
> Cells Biology, Stem Cells, and Development Program
> Dr. David Clouthier lab, Craniofacial Biology
>
> For Correspondence:
> University of Colorado, Health Sciences Center
> Department of Craniofacial Biology
> Mailstop 8120
> P.O. Box 6511
> Aurora, CO 80045
>
> For Deliveries:
> University of Colorado Denver Health Sciences Center
> Department of Craniofacial Biology
> Building RC1 South, Room 11400B
> 12801 East 17th Avenue
> Aurora, Co 80010
>
> Lab: 303-724-4566
> Fax: 303-724-4580
>
> *****************************************************************
>
> ________________________________________
> From: Daniel James White [
[hidden email]]
> Sent: Wednesday, July 07, 2010 9:18 AM
> To: Barron, Francie
> Subject: Re:Automatic Cell Counting
>
> to me!
>
>
[hidden email]
>
> just reply to this emial
>
> Dan
>
>
> On Jul 7, 2010, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
>> Date: Tue, 6 Jul 2010 10:07:46 -0600
>> From: "Barron, Francie" <
[hidden email]>
>> Subject: Re: Automatic Cell Counting
>>
>> Hi Dan,
>>
>> What is the email I can send the information to?
>>
>> Thanks,
>> ~Francie
>>
>> NOTE NEW EMAIL ADDRESS:
[hidden email]
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
>
http://www.bioimagexd.net BioImageXD
>
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
>
http://www.chalkie.org.uk Dan's Homepages
>
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
>
>
>
>
>
>
>
>
>
>
> <DAPImontage.jpg><REDmontage.jpg>
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)
http://www.bioimagexd.net BioImageXD
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )