Is there an ImageJ plugin available for OSX?

Bayesian analysis of blinking and bleaching

Is there an ImageJ plugin available for OSX?

Postby Sam » Fri Mar 01, 2013 12:35 am

Is there an ImageJ plugin available for OSX?
Sam
 
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Re: Is there an ImageJ plugin available for OSX?

Postby edrosten » Fri Mar 01, 2013 5:33 pm

Sam wrote:Is there an ImageJ plugin available for OSX?


Producing plugin for OSX is on our todo list.

In the mean time, the standalone commandline program will compile and run on OSX, and also you will be able to use the 3B plugin on OSX to load 3B runs done by the standalone program.

We will make an announcement when the OSX plugin is available. Please send me an email if you wish to be notified by email when the plugin is released.
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Re: Is there an ImageJ plugin available for OSX?

Postby Sam » Sat Mar 02, 2013 2:53 pm

Great - I'll send you my email address
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Re: Is there an ImageJ plugin available for OSX?

Postby adson3492 » Fri Nov 14, 2014 10:18 am

Hi again!
It is actually quite neat to have the control panel, and is very useful to set the reconstruction blur FWHM to see the effect on each reconstruction. However once I've decided for a certain blur, I was wondering if there was a way to open directly an image file without going trough the control panel. I reckon it would be very useful for a macro that I'm writing which automatically assembles 3B reconstructions of small contiguous ROIs into a larger reconstructed area.
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Re: Is there an ImageJ plugin available for OSX?

Postby edrosten » Tue Nov 25, 2014 1:44 pm

Hi,

There's two aspects t what you're doing: performing the analysis and doing the reconstruction.

In the first case, 3B should work with macros so setting them running with a script should be OK. If it's not, then there's a bug, so let me know.

In the latter case, I couldn't figure out how to make the built in dialogs do what I wanted, so it's not scriptable. However, it offers something a bit better (I think). If you concatenate all the files together into a single large file and load that, it will reconstruct them all together into the appropriate sized region (it will take a union of the regions).

We've also been working on some software to do he following:
1. Take a large region and split it up into small squares
2. Dilate the squares slightly so the borders overlap
3. (run 3B on all the squares--this bit is currently left up to the user)
4. paste together all the reconstructions, discarding the border regions.

For the commandline version, we have software that does 1,2 and 4. 3 usually requires a cluster due to the large computational costs, os we don't have anything for that as clustering software is too varied.

There are more detail here: viewtopic.php?p=30809#p30809

You'll need a beta release of the software. Let me know if you have any questions.


-Ed
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