MultiRoi viewer

[Frederick Ross]

I've just finished putting together an extension to the normal
StackWindow which handles multiple Rois sensibly.  It uses the right
button to handle selecting deselecting, and the left button only for
manipulating the current Roi (or whatever else it may do...I don't
intercept anything else).  There is one nice side effect that you
don't lose an Roi if you click outside of it by accident.

This is something people have asked about fairly regularly, so I
thought I'd post it.

It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi

--
Frederick Ross
Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
The Rockefeller University
Je ne suis pas Fred Cross!

[Philip Ershler]

This sounds like a nice tool. However I followed the instructions on  
wiki referenced below and here's what I get when I try to run Multi-
Roi in ImageJ 1.38P

Plugin or class not found: "MultiRoi"
(java.lang.NoClassDefFoundError: com/vividsolutions/jts/geom/Geometry)

Any suggestions?

Thanks, Phil

On Apr 26, 2007, at 1:16 PM, Frederick Ross wrote:

> I've just finished putting together an extension to the normal
> StackWindow which handles multiple Rois sensibly.  It uses the right
> button to handle selecting deselecting, and the left button only for
> manipulating the current Roi (or whatever else it may do...I don't
> intercept anything else).  There is one nice side effect that you
> don't lose an Roi if you click outside of it by accident.
>
> This is something people have asked about fairly regularly, so I
> thought I'd post it.
>
> It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi
>
> --
> Frederick Ross
> Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> The Rockefeller University
> Je ne suis pas Fred Cross!

[Frederick Ross]

Whoops!  Yes, sorry, forgot to add that to the README.  It requires
the Java Topology Suite to judge interiors/exteriors of regions.  You
can download it from http://www.vividsolutions.com/jts/jtshome.htm

> Any suggestions?
>
> Thanks, Phil
>
> On Apr 26, 2007, at 1:16 PM, Frederick Ross wrote:
>
> > I've just finished putting together an extension to the normal
> > StackWindow which handles multiple Rois sensibly.  It uses the right
> > button to handle selecting deselecting, and the left button only for
> > manipulating the current Roi (or whatever else it may do...I don't
> > intercept anything else).  There is one nice side effect that you
> > don't lose an Roi if you click outside of it by accident.
> >
> > This is something people have asked about fairly regularly, so I
> > thought I'd post it.
> >
> > It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi
> >
> > --
> > Frederick Ross
> > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> > The Rockefeller University
> > Je ne suis pas Fred Cross!
>

--
Frederick Ross
Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
The Rockefeller University
Je ne suis pas Fred Cross!

[Brent Wood]

Hi,

We are using ImageJ for identifying & quantifying taxa & substrates
captured in seabed photos.

To improve this process we are looking to have the image metadata
managed in a PostGIS (Postgres) database, and have ImageJ interact with
this database, to select & load images, & to directly store counts,
measurements & ROI's derived from the images in this database.

We have a contractor to undertake this for us, but if anyone here would
like to contribute ideas/experiences which would help us with this, or
would help us create a more generically useful application, please let
me know.


Cheers,

  Brent Wood

[Philip Ershler]

Sorry to be such a pest, but what do I do with the folder and/or  
files that I downloaded from Vivid Solutions?

Thanks, Phil

On Apr 26, 2007, at 2:50 PM, Frederick Ross wrote:

> Whoops!  Yes, sorry, forgot to add that to the README.  It requires
> the Java Topology Suite to judge interiors/exteriors of regions.  You
> can download it from http://www.vividsolutions.com/jts/jtshome.htm
>
>> Any suggestions?
>>
>> Thanks, Phil
>>
>> On Apr 26, 2007, at 1:16 PM, Frederick Ross wrote:
>>
>> > I've just finished putting together an extension to the normal
>> > StackWindow which handles multiple Rois sensibly.  It uses the  
>> right
>> > button to handle selecting deselecting, and the left button only  
>> for
>> > manipulating the current Roi (or whatever else it may do...I don't
>> > intercept anything else).  There is one nice side effect that you
>> > don't lose an Roi if you click outside of it by accident.
>> >
>> > This is something people have asked about fairly regularly, so I
>> > thought I'd post it.
>> >
>> > It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi
>> >
>> > --
>> > Frederick Ross
>> > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
>> > The Rockefeller University
>> > Je ne suis pas Fred Cross!
>>
>
>
> --
> Frederick Ross
> Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> The Rockefeller University
> Je ne suis pas Fred Cross!

Philip R. Ershler Ph.D.
University of Utah
Cardiovascular Research and Training Institute
95 South 2000 East
Salt Lake City, UT 84112-5000

phone: [phone]
alt ph: [phone]
fax: [phone]
e-mail: [hidden email]

[Frederick Ross]

In the lib/ directory inside, you'll find jts.jar and jtsio.jar.  Put
them in the ext/ directory of your JDK (on linux it's usually
/usr/lib/jvm/jdk-(version)/ext.

On 4/26/07, Philip Ershler <[hidden email]> wrote:

> Sorry to be such a pest, but what do I do with the folder and/or
> files that I downloaded from Vivid Solutions?
>
> Thanks, Phil
>
> On Apr 26, 2007, at 2:50 PM, Frederick Ross wrote:
>
> > Whoops!  Yes, sorry, forgot to add that to the README.  It requires
> > the Java Topology Suite to judge interiors/exteriors of regions.  You
> > can download it from http://www.vividsolutions.com/jts/jtshome.htm
> >
> >> Any suggestions?
> >>
> >> Thanks, Phil
> >>
> >> On Apr 26, 2007, at 1:16 PM, Frederick Ross wrote:
> >>
> >> > I've just finished putting together an extension to the normal
> >> > StackWindow which handles multiple Rois sensibly.  It uses the
> >> right
> >> > button to handle selecting deselecting, and the left button only
> >> for
> >> > manipulating the current Roi (or whatever else it may do...I don't
> >> > intercept anything else).  There is one nice side effect that you
> >> > don't lose an Roi if you click outside of it by accident.
> >> >
> >> > This is something people have asked about fairly regularly, so I
> >> > thought I'd post it.
> >> >
> >> > It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi
> >> >
> >> > --
> >> > Frederick Ross
> >> > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> >> > The Rockefeller University
> >> > Je ne suis pas Fred Cross!
> >>
> >
> >
> > --
> > Frederick Ross
> > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> > The Rockefeller University
> > Je ne suis pas Fred Cross!
>
> Philip R. Ershler Ph.D.
> University of Utah
> Cardiovascular Research and Training Institute
> 95 South 2000 East
> Salt Lake City, UT 84112-5000
>
> phone: [phone]
> alt ph: [phone]
> fax: [phone]
> e-mail: [hidden email]
>

--
Frederick Ross
Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
The Rockefeller University
Je ne suis pas Fred Cross!

[Albert Cardona]

Hi Brent,

If you need help on how to make ImageJ interact with PostgreSQL, the
ini.persistence.DBLoader class from TrakEM2 (
http://www.ini.uzh.ch/~acardona/trakem2.html ) may provide you with a
tone of hints.

The DBLoader represents one of the two modes in which TrakEM2 can
operate, and stores *everything* in the database, including images,
scaled snapshots of images and edited versions, in a bytea column.

On PostGIS: I didn't know it existed, thanks for the link.

Albert

[James Norman]

You can also put the files in the ImageJ/plugins directory.  ImageJ
should load all the classes in the plugins directory.

-james

On 4/26/07, Frederick Ross <[hidden email]> wrote:

> In the lib/ directory inside, you'll find jts.jar and jtsio.jar.  Put
> them in the ext/ directory of your JDK (on linux it's usually
> /usr/lib/jvm/jdk-(version)/ext.
>
> On 4/26/07, Philip Ershler <[hidden email]> wrote:
> > Sorry to be such a pest, but what do I do with the folder and/or
> > files that I downloaded from Vivid Solutions?
> >
> > Thanks, Phil
> >
> > On Apr 26, 2007, at 2:50 PM, Frederick Ross wrote:
> >
> > > Whoops!  Yes, sorry, forgot to add that to the README.  It requires
> > > the Java Topology Suite to judge interiors/exteriors of regions.  You
> > > can download it from http://www.vividsolutions.com/jts/jtshome.htm
> > >
> > >> Any suggestions?
> > >>
> > >> Thanks, Phil
> > >>
> > >> On Apr 26, 2007, at 1:16 PM, Frederick Ross wrote:
> > >>
> > >> > I've just finished putting together an extension to the normal
> > >> > StackWindow which handles multiple Rois sensibly.  It uses the
> > >> right
> > >> > button to handle selecting deselecting, and the left button only
> > >> for
> > >> > manipulating the current Roi (or whatever else it may do...I don't
> > >> > intercept anything else).  There is one nice side effect that you
> > >> > don't lose an Roi if you click outside of it by accident.
> > >> >
> > >> > This is something people have asked about fairly regularly, so I
> > >> > thought I'd post it.
> > >> >
> > >> > It's at http://www.openwetware.org/wiki/Madhadron:MultiRoi
> > >> >
> > >> > --
> > >> > Frederick Ross
> > >> > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> > >> > The Rockefeller University
> > >> > Je ne suis pas Fred Cross!
> > >>
> > >
> > >
> > > --
> > > Frederick Ross
> > > Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> > > The Rockefeller University
> > > Je ne suis pas Fred Cross!
> >
> > Philip R. Ershler Ph.D.
> > University of Utah
> > Cardiovascular Research and Training Institute
> > 95 South 2000 East
> > Salt Lake City, UT 84112-5000
> >
> > phone: [phone]
> > alt ph: [phone]
> > fax: [phone]
> > e-mail: [hidden email]
> >
>
>
> --
> Frederick Ross
> Graduate Fellow, (|Siggia> + |McKinney>)/sqrt(2) Lab
> The Rockefeller University
> Je ne suis pas Fred Cross!
>