colony counting

[Pieter Coussement]

Hi
I have a question about colony counting.

First of all, i know there is plugin. But it doesn't always count properly.
When I select my agar plate and do the 'clear outside' thing, then it
still tend so count some squares at the side of the agar plate.

Second i would like to count two different colors of bacteria. I've got
white ones and red/pijnk ones. I would like to know how many of both
there are on the plate.

Any help?

kind regards
Pieter

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[Krs5]

Hi Pieter,

I don't know about the colony counting plugin but for the separation of white and red/pink colonies you could run Image > Color > Split Channels. I would expect your white colonies in all three images and your red/pink in the blue and red channels. Subtract green from red (Process > Image calculator) should hopefully give the white colonies. Maybe it is possible to count them after thresholding?

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
University of Leicester
http://www.le.ac.uk/biochem/microscopy/home.html

20-24 August fluorescence microscopy workshops: http://www.le.ac.uk/biochem/microscopy/workshop2012.html


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Pieter Coussement
Sent: 25 July 2012 14:54
To: [hidden email]
Subject: colony counting

Hi
I have a question about colony counting.

First of all, i know there is plugin. But it doesn't always count properly.
When I select my agar plate and do the 'clear outside' thing, then it
still tend so count some squares at the side of the agar plate.

Second i would like to count two different colors of bacteria. I've got
white ones and red/pijnk ones. I would like to know how many of both
there are on the plate.

Any help?

kind regards
Pieter

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[LIM Soon Yew John (IMB)]

Hi Peter,

For your first problem, you could first threshold your colonies, then create an ROI around the edge of your plate and use the Analyze Particles command with the option "Exclude on edges".

For your second problem, you could threshold the image using Image>Adjust>Color Threshold or Image>Color>Color Deconvolution (In Fiji) to separate the pink and white colonies.

Best Regards
John

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Pieter Coussement [[hidden email]]
Sent: Wednesday, July 25, 2012 9:53 PM
To: [hidden email]
Subject: colony counting

Hi
I have a question about colony counting.

First of all, i know there is plugin. But it doesn't always count properly.
When I select my agar plate and do the 'clear outside' thing, then it
still tend so count some squares at the side of the agar plate.

Second i would like to count two different colors of bacteria. I've got
white ones and red/pijnk ones. I would like to know how many of both
there are on the plate.

Any help?

kind regards
Pieter

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html