Acquisition Plugin for Confocal Microscopy

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Acquisition Plugin for Confocal Microscopy

Tom Harris-6
Greetings

Years ago I used NIH image to view images captured on a confocal
microscope. Now I find myself looking at building a new confocal system
from the ground up (with some help naturally), and I would like to write
an ImageJ plugin to habdle the acquisition part, so that I can use the
power of ImageJ to process & view the images. In common with other
confocal systems, the images are 12 bit multi plane, as single images or
stacks.

Last time I looked NIH image did not handle multiplane images of more than
8 bits/plane very well, but I think that this has changed.

Am I fooling myself? What is a good acquisition plugin to study? I have
ordered the Burger book. I have never used Java, but I have about 10 years
with C++ & Python, so I think that I can pick it up as I go along.

Someone give me some encoragement, as I can't bear writing yet another
image processing/display application.

TomH
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Re: Acquisition Plugin for Confocal Microscopy

ctrueden
Hi Tom,

Did you check out the open source Micro-Manager project? Its GUI is
ImageJ-based, so you get all that functionality too:
http://micro-manager.org/

I suggest checking the list of devices to see whether the hardware you want
to use is supported:
http://micro-manager.org/documentation.php?object=DeviceDir

At this point, with your enthusiasm and experience, you will almost
certainly be able to get something going without needing to code any
acquisition, visualization or analysis software from scratch. If
Micro-Manager won't work for you for some reason, just follow up here with
details and I'm sure people can point you in a good direction from there.

Good luck,
Curtis

On Sun, Apr 13, 2008 at 4:40 AM, Tom Harris <[hidden email]> wrote:

> Greetings
>
> Years ago I used NIH image to view images captured on a confocal
> microscope. Now I find myself looking at building a new confocal system
> from the ground up (with some help naturally), and I would like to write
> an ImageJ plugin to habdle the acquisition part, so that I can use the
> power of ImageJ to process & view the images. In common with other
> confocal systems, the images are 12 bit multi plane, as single images or
> stacks.
>
> Last time I looked NIH image did not handle multiplane images of more than
> 8 bits/plane very well, but I think that this has changed.
>
> Am I fooling myself? What is a good acquisition plugin to study? I have
> ordered the Burger book. I have never used Java, but I have about 10 years
> with C++ & Python, so I think that I can pick it up as I go along.
>
> Someone give me some encoragement, as I can't bear writing yet another
> image processing/display application.
>
> TomH
>