RATS implementation

[Ben Tupper]

Hi All,

I have not found any references to implementations of the Robust  
Automatic Threshold Selection (aka RATS) algorithm in ImageJ (or  
Java).  We have used this with great success with fluorescent  
microscopy in the past in IDL, but would love to have access to it  
via ImageJ. Anybody heard of it before?

Here is a general description for Michael Wilkinson...
http://www.cs.rug.nl/~michael/teaching/mlrats.html

And here is a much more detailed description by Gaetan Lehmann...
http://www.insight-journal.org/InsightJournalManager/publications.php?
journalid=6

The challenging part (for me) is that the image is regionalized using  
quadtrees - which I have implemented in IDL before, but might require  
something close to a miracle for me to whip up in Java. I would love  
to avoid reinventing the wheel if it already exists (and wheels that  
I make never come out all that round!)

Thanks for any pointers.

Ben

Ben Tupper
[hidden email]

I GoodSearch for Ashwood Waldorf School.

Raise money for your favorite charity or school just by searching the  
Internet with GoodSearch - www.goodsearch.com - powered by Yahoo!

[ctrueden]

Hi Ben,

A quick Google search for quadtree java yields source code and/or
javadocs for multiple distinct implementations. Perhaps one of those
would work for you.

-Curtis

On Nov 21, 2007 12:29 PM, Ben Tupper <[hidden email]> wrote:

> Hi All,
>
> I have not found any references to implementations of the Robust
> Automatic Threshold Selection (aka RATS) algorithm in ImageJ (or
> Java).  We have used this with great success with fluorescent
> microscopy in the past in IDL, but would love to have access to it
> via ImageJ. Anybody heard of it before?
>
> Here is a general description for Michael Wilkinson...
> http://www.cs.rug.nl/~michael/teaching/mlrats.html
>
> And here is a much more detailed description by Gaetan Lehmann...
> http://www.insight-journal.org/InsightJournalManager/publications.php?
> journalid=6
>
> The challenging part (for me) is that the image is regionalized using
> quadtrees - which I have implemented in IDL before, but might require
> something close to a miracle for me to whip up in Java. I would love
> to avoid reinventing the wheel if it already exists (and wheels that
> I make never come out all that round!)
>
> Thanks for any pointers.
>
> Ben
>
> Ben Tupper
> [hidden email]
>
> I GoodSearch for Ashwood Waldorf School.
>
> Raise money for your favorite charity or school just by searching the
> Internet with GoodSearch - www.goodsearch.com - powered by Yahoo!
>

... [show rest of quote]

[Ben Tupper]

On Nov 21, 2007, at 1:45 PM, Curtis Rueden wrote:

> Hi Ben,
>
> A quick Google search for quadtree java yields source code and/or
> javadocs for multiple distinct implementations. Perhaps one of those
> would work for you.
>

Thanks Curtis,

I have been eyeballing some of the examples out there.  Here is one  
that draws my eye... http://tinyurl.com/2aqeqn  I had hopes of  
finding an ImageJ-centric implementation of a quadtree - something  
that already exploits ImageJ's Roi object and graphics.  I'll give it  
a whack sometime soon.

Cheers,
Ben

> -Curtis
>
> On Nov 21, 2007 12:29 PM, Ben Tupper <[hidden email]>  
> wrote:
>> Hi All,
>>
>> I have not found any references to implementations of the Robust
>> Automatic Threshold Selection (aka RATS) algorithm in ImageJ (or
>> Java).  We have used this with great success with fluorescent
>> microscopy in the past in IDL, but would love to have access to it
>> via ImageJ. Anybody heard of it before?
>>
>> Here is a general description for Michael Wilkinson...
>> http://www.cs.rug.nl/~michael/teaching/mlrats.html
>>
>> And here is a much more detailed description by Gaetan Lehmann...
>> http://www.insight-journal.org/InsightJournalManager/ 
>> publications.php?
>> journalid=6
>>
>> The challenging part (for me) is that the image is regionalized using
>> quadtrees - which I have implemented in IDL before, but might require
>> something close to a miracle for me to whip up in Java. I would love
>> to avoid reinventing the wheel if it already exists (and wheels that
>> I make never come out all that round!)
>>
>> Thanks for any pointers.
>>
>> Ben
>>
>> Ben Tupper
>> [hidden email]
>>
>> I GoodSearch for Ashwood Waldorf School.
>>
>> Raise money for your favorite charity or school just by searching the
>> Internet with GoodSearch - www.goodsearch.com - powered by Yahoo!
>>

... [show rest of quote]

Ben Tupper
[hidden email]

I GoodSearch for Ashwood Waldorf School.

Raise money for your favorite charity or school just by searching the  
Internet with GoodSearch - www.goodsearch.com - powered by Yahoo!