Questio on counting bacterial cells on an alga surface

[Stephanie Stratil]

Dear all,

 

I am a PhD student in the field of marine ecology. My aim is to quantify
DAPI stained bacterial cells on macroalgae surfaces. For this purpose I took
Z stack images of the alga surface from which I would like to count the
bacterial cells using Image J.

 

Unfortunately, the algal cells have a bright autofluorescence and an uneven
surface topography and thus create a lot of background noise in many slices
of a stack. This makes it very difficult to subtract the background and set
a correct threshold without “losing” bacterial cells in the process. Are you
aware of any solutions to this problem (e.g.  subtraction of the algal
cells)?

 

I have placed two representative images in a Dropbox folder under following

link:

 

https://www.dropbox.com/sh/oowzz4jzy0ae4os/rR698CtO1T

 

I am looking forward to any advice on this matter.

 

Thank you very much

 

Cheers,

Stephanie

 

 

Dipl.-Biol. Stephanie Stratil

Benthic Ecology (EÖB)

Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR)

Düsternbrooker Weg 20

24105 Kiel, Germany

 

Tel. [phone]

 <mailto:[hidden email]> [hidden email]

 <http://www.geomar.de/> www.geomar.de

 


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[Christine Labno]

Hi Stephanie,

Have you tried a bandpass filter?  It's found under Process -> FFT -> Bandpass filter.  

On your alga I stack (converted to a 16-bit .tif file) I found that filtering down to 10 and up to 3 pixels effectively suppressed much of the larger algal cell signal while preserving the shape and signal of the smaller bacterial cells.  

Best,
Christine

Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
[phone] (phone)
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---- Original message ----

>Date: Wed, 13 Jun 2012 15:02:11 +0200
>From: ImageJ Interest Group <[hidden email]> (on behalf of Stephanie Stratil <[hidden email]>)
>Subject: Questio on counting bacterial cells on an alga surface  
>To: <[hidden email]>
>
>Dear all,
>
>
>
>I am a PhD student in the field of marine ecology. My aim is to quantify
>DAPI stained bacterial cells on macroalgae surfaces. For this purpose I took
>Z stack images of the alga surface from which I would like to count the
>bacterial cells using Image J.
>
>
>
>Unfortunately, the algal cells have a bright autofluorescence and an uneven
>surface topography and thus create a lot of background noise in many slices
>of a stack. This makes it very difficult to subtract the background and set
>a correct threshold without “losing” bacterial cells in the process. Are you
>aware of any solutions to this problem (e.g.  subtraction of the algal
>cells)?
>
>
>
>I have placed two representative images in a Dropbox folder under following
>
>link:
>
>
>
>https://www.dropbox.com/sh/oowzz4jzy0ae4os/rR698CtO1T
>
>
>
>I am looking forward to any advice on this matter.
>
>
>
>Thank you very much
>
>
>
>Cheers,
>
>Stephanie
>
>
>
>
>
>Dipl.-Biol. Stephanie Stratil
>
>Benthic Ecology (EÖB)
>
>Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR)
>
>Düsternbrooker Weg 20
>
>24105 Kiel, Germany
>
>
>
>Tel. [phone]
>
> <mailto:[hidden email]> [hidden email]
>
> <http://www.geomar.de/> www.geomar.de
>
>
>
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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