Re: Automatic Nuclei Counter plug-in for ImageJ - ITCN Plugin

Posted by Jacqueline Ross on Oct 30, 2014; 9:16pm
URL: http://imagej.273.s1.nabble.com/Automatic-Nuclei-Counter-plug-in-for-ImageJ-ITCN-Plugin-tp5010217p5010254.html

Thanks Kees,

I'll try it out!

Much appreciated.

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 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

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

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straatman, Kees (Dr.)
Sent: Thursday, 30 October 2014 10:19 p.m.
To: [hidden email]
Subject: Re: Automatic Nuclei Counter plug-in for ImageJ - ITCN Plugin

Hi Jacqui,

Please see attached screen shot. Don't forget to select 'Detect Dark Peaks' if you have dark stained nuclei like DAB staining. If wrongly selected I get peaks in between my nuclei. In some cases we set a threshold of 0 if no nuclei are found at all. Hopes this helps to solve the problem.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif

ImageJ workshops 15 and 16 December


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacqui Ross
Sent: 29 October 2014 21:30
To: [hidden email]
Subject: Re: Automatic Nuclei Counter plug-in for ImageJ - ITCN Plugin

Hi Kees,

Thanks very much for your reply. Usually, I get zero cells detected or some other number which doesn't relate to the actual number of nuclei present. When I get a result, e.g. 90 nuclei, the red spots which I assume are positioned at the centre of the where each nucleus has been detected are located in the middle of nowhere, i.e. not on nuclei but some point in between.

Are you able to send me a sample image and the values that you used for it so that I can do some testing?

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 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

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

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straatman, Kees (Dr.)
Sent: Wednesday, 29 October 2014 9:32 p.m.
To: [hidden email]
Subject: Re: Automatic Nuclei Counter plug-in for ImageJ - ITCN Plugin

Hi Jacqui,

Users in my facility have used this plugin with good results. The threshold does not show anything in the active image but as far as I remember we use in most cases a value of 0.1. The values for with we measure from the image and the rest seems to go automatically. What are the results you get?

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif
ImageJ workshops 15 and 16 December

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacqui Ross
Sent: 29 October 2014 04:02
To: [hidden email]
Subject: Automatic Nuclei Counter plug-in for ImageJ - ITCN Plugin

Hi all,

I'm looking for some help with the ITCN plugin. One of our users sent me a link to the plugin and it looks like it might be quite useful. However, I can't seem to get it to work properly.

I entered values for the Width of the nuclei and Minimum distance and have tried various threshold values without success. When I move the threshold slider nothing changes on my image. I thought it should give some indication of the nuclei that are identified.

The instructions on the website look good http://www.bioimage.ucsb.edu/automatic-nuclei-counter-plug-in-for-imagej but I can't get it to work for me even with giant nuclei that are very obvious. I haven't been able to download the example images for some reason.

I'm running Windows 7 64 bit ImageJ version 1.49f. Haven't tried it with FIJI yet.

Can anyone help me out with this?

Cheers,

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 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

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


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