Re : Custom build bacterial colony counter hardware.

[ssim]

Dear lists,

I think my question is irrelevant to the list, but I thought I ask anyway,
as i don't know who to turn to.

I have written a plugin performing automated bacterial colony counts
(Streptococus Uberis) using ImageJ (accredited to ImageJ's user list).
However, I constantly encountered image's quality issues like uneven shadow
from the rim of the dish, levelness of the dish divider and constrast. The
tools used to photograph the dish are very primitive( a digital camera,
lightbox and tripod). The lab technician set up the equipments in every
photograph session, and pack them away after finish. The variations in
every photograph session were visible in the images (despite  in their best
effort to keep everything consistent). There is no control of the natural
lighting at all. I want to build them a custom lightbox with a camera
moulded on top ... Have anyone attempt that ? Any suggestions are welcome !
FYI, Purschasing a colony counter hardware is out of question.

Thanks in advance.

Stella

[Olivier Salvado]

We got around the same problem although for a different setup by shooting at
each session a calibration phantom.

Briefly:
We shoot a white paper (you don't want a specular material) that we put in
place of the sample.
We tune the exposure and the white balance of the camera on the white
phantom.
Each subsequent image is corrected for background illumination using the
white paper.
We found the method simple yet very powerful.

White balance and exposure can be performed by image processing if not
easily feasible on the camera itself.

Olivier Salvado

 
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Stella
Sim
Sent: Sunday, January 22, 2006 4:58 PM
To: [hidden email]
Subject: Re : Custom build bacterial colony counter hardware.

Dear lists,

I think my question is irrelevant to the list, but I thought I ask anyway,
as i don't know who to turn to.

I have written a plugin performing automated bacterial colony counts
(Streptococus Uberis) using ImageJ (accredited to ImageJ's user list).
However, I constantly encountered image's quality issues like uneven shadow
from the rim of the dish, levelness of the dish divider and constrast. The
tools used to photograph the dish are very primitive( a digital camera,
lightbox and tripod). The lab technician set up the equipments in every
photograph session, and pack them away after finish. The variations in
every photograph session were visible in the images (despite  in their best
effort to keep everything consistent). There is no control of the natural
lighting at all. I want to build them a custom lightbox with a camera
moulded on top ... Have anyone attempt that ? Any suggestions are welcome !
FYI, Purschasing a colony counter hardware is out of question.

Thanks in advance.

Stella

[dksamuel]

I would like to receive a copy of the plugin regards Samuel

On 1/23/06, Olivier Salvado <[hidden email]> wrote:

>
> We got around the same problem although for a different setup by shooting
> at
> each session a calibration phantom.
>
> Briefly:
> We shoot a white paper (you don't want a specular material) that we put in
> place of the sample.
> We tune the exposure and the white balance of the camera on the white
> phantom.
> Each subsequent image is corrected for background illumination using the
> white paper.
> We found the method simple yet very powerful.
>
> White balance and exposure can be performed by image processing if not
> easily feasible on the camera itself.
>
> Olivier Salvado
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Stella
> Sim
> Sent: Sunday, January 22, 2006 4:58 PM
> To: [hidden email]
> Subject: Re : Custom build bacterial colony counter hardware.
>
> Dear lists,
>
> I think my question is irrelevant to the list, but I thought I ask anyway,
> as i don't know who to turn to.
>
> I have written a plugin performing automated bacterial colony counts
> (Streptococus Uberis) using ImageJ (accredited to ImageJ's user list).
> However, I constantly encountered image's quality issues like uneven
> shadow
> from the rim of the dish, levelness of the dish divider and constrast. The
> tools used to photograph the dish are very primitive( a digital camera,
> lightbox and tripod). The lab technician set up the equipments in every
> photograph session, and pack them away after finish. The variations in
> every photograph session were visible in the images (despite  in their
> best
> effort to keep everything consistent). There is no control of the natural
> lighting at all. I want to build them a custom lightbox with a camera
> moulded on top ... Have anyone attempt that ? Any suggestions are welcome
> !
> FYI, Purschasing a colony counter hardware is out of question.
>
> Thanks in advance.
>
> Stella
>

[Olivier Salvado]

We don't use a particular plug-in, just regular operations and a script in
Matlab for batch processing.

Olivier Salvado

 
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Duleep
Samuel
Sent: Sunday, January 22, 2006 10:51 PM
To: [hidden email]
Subject: Re: Custom build bacterial colony counter hardware.

I would like to receive a copy of the plugin regards Samuel

On 1/23/06, Olivier Salvado <[hidden email]> wrote:

>
> We got around the same problem although for a different setup by shooting
> at
> each session a calibration phantom.
>
> Briefly:
> We shoot a white paper (you don't want a specular material) that we put in
> place of the sample.
> We tune the exposure and the white balance of the camera on the white
> phantom.
> Each subsequent image is corrected for background illumination using the
> white paper.
> We found the method simple yet very powerful.
>
> White balance and exposure can be performed by image processing if not
> easily feasible on the camera itself.
>
> Olivier Salvado
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Stella
> Sim
> Sent: Sunday, January 22, 2006 4:58 PM
> To: [hidden email]
> Subject: Re : Custom build bacterial colony counter hardware.
>
> Dear lists,
>
> I think my question is irrelevant to the list, but I thought I ask anyway,
> as i don't know who to turn to.
>
> I have written a plugin performing automated bacterial colony counts
> (Streptococus Uberis) using ImageJ (accredited to ImageJ's user list).
> However, I constantly encountered image's quality issues like uneven
> shadow
> from the rim of the dish, levelness of the dish divider and constrast. The
> tools used to photograph the dish are very primitive( a digital camera,
> lightbox and tripod). The lab technician set up the equipments in every
> photograph session, and pack them away after finish. The variations in
> every photograph session were visible in the images (despite  in their
> best
> effort to keep everything consistent). There is no control of the natural
> lighting at all. I want to build them a custom lightbox with a camera
> moulded on top ... Have anyone attempt that ? Any suggestions are welcome
> !
> FYI, Purschasing a colony counter hardware is out of question.
>
> Thanks in advance.
>
> Stella
>