new to list

[Hunt, Jason]

I'm new to the list and hope that I don't jeopardize my new status by sending this e mail to 10,000 users but I'm in a bit of a crunch and need some quick advice. I would like to analyze the amount of PAS staining (staining for glycogen) in histological images. Not too hard if I convert the image to black and white, the problem is that I also stained with H and E and when I convert to grayscale the nuclei stand out and PAS staining is no longer visible. I have to be able to somehow tell the computer to look for the magenta color of the PAS staining and nothing else? Is this possible? I've read about every manual I can find on line for Image J and it seems like it is possible but apparently I'm not smart enough to figure it out. Can anyone help.

Thank you very much in advance.

Jason

[daschneider9]

Jason,

I wonder if you couldn't use the "Colour Deconvolution" plugin for this. Information on it can be found here: http://imagejdocu.tudor.lu/doku.php?id=plugin:color:colour_deconvolution:start

That link will provide you with more links including the download site.

I too am new so take this suggestion with a grain of salt.

Regards,
Dave
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Hunt, Jason
Sent: Friday, February 05, 2010 4:06 PM
To: [hidden email]
Subject: new to list


I'm new to the list and hope that I don't jeopardize my new status by sending this e mail to 10,000 users but I'm in a bit of a crunch and need some quick advice. I would like to analyze the amount of PAS staining (staining for glycogen) in histological images. Not too hard if I convert the image to black and white, the problem is that I also stained with H and E and when I convert to grayscale the nuclei stand out and PAS staining is no longer visible. I have to be able to somehow tell the computer to look for the magenta color of the PAS staining and nothing else? Is this possible? I've read about every manual I can find on line for Image J and it seems like it is possible but apparently I'm not smart enough to figure it out. Can anyone help.

Thank you very much in advance.

Jason

[Jacqueline Ross]

Hi Jason,

Colour deconvolution may well work for you as suggested by Dave.

You could also try the Threshold Colour plugin
(http://www.dentistry.bham.ac.uk/landinig/software/software.html  on
Gabriel Landini's website.

There are also some instructions on our website for this and the Colour
Decon if you run into difficulties.

Kind regards,

Jacqui.

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Hunt, Jason
Sent: Saturday, 6 February 2010 1:06 p.m.
To: [hidden email]
Subject: new to list


I'm new to the list and hope that I don't jeopardize my new status by
sending this e mail to 10,000 users but I'm in a bit of a crunch and
need some quick advice. I would like to analyze the amount of PAS
staining (staining for glycogen) in histological images. Not too hard if
I convert the image to black and white, the problem is that I also
stained with H and E and when I convert to grayscale the nuclei stand
out and PAS staining is no longer visible. I have to be able to somehow
tell the computer to look for the magenta color of the PAS staining and
nothing else? Is this possible? I've read about every manual I can find
on line for Image J and it seems like it is possible but apparently I'm
not smart enough to figure it out. Can anyone help.

Thank you very much in advance.

Jason