Re: Fiji gets stuck at Trainable Weka Segmentation

Posted by Ignacio Arganda-Carreras on Mar 27, 2014; 9:25am
URL: http://imagej.273.s1.nabble.com/Fiji-gets-stuck-at-Trainable-Weka-Segmentation-tp5007076p5007099.html

Dear Xiaoxiong,


> I am running Scientific Linux 6.0, 64 bit version. The data is composed of
> 738 slices of 738*738 8 bit images, in total about 400 MB, but I am using a
> high performance machine which contains 16 CPUs and 128 GB memory, so it
> shouldn't be the problem.
>

I see. Do you train on an image of that size? Or you want to apply a
trained classifier on such an image?

You might be interested on Larry LIndsey's plugin to run the classifier in
a cluster: http://fiji.sc/Fiji_Archipelago


>
> Today I found that Fiji Weka plugin got stuck if it tried to process a
> black image and if I removed the black images, it then can move forward. I
> am not sure if it's a bug of the plugin.
>
>
Weird! Cand you send me a couple of the slices (some black ones too) to
reproduce the error in my machine?


> Thanks a lot.
>

Thank you for reporting!

ignacio

> Xiaoxiong
>
>
> 2014-03-26 3:41 GMT-06:00 Ignacio Arganda-Carreras <
> [hidden email]>:
>
> > Dear Xiaoxiong,
> >
> > Can you tell us more about the problem? What is the size of the image
> > you're using? Your system (Linux, Mac, Windows)? 32 or 64 bit? Your RAM?
> >
> > Thanks!
> >
> > ignacio
> >
> >
> > On Tue, Mar 25, 2014 at 8:18 PM, Xiaoxiong Xing <[hidden email]
> > >wrote:
> >
> > > Dear users,
> > >
> > > My Fiji sometimes gets stuck at "*Filtering feature stack by selected
> > > attributes...*" when I try to apply a classifier to a new image or an
> > image
> > > stack. However, the same operation sometimes works fine, which makes me
> > > fill weird.
> > >
> > > Are there anyone have the same problem?
> > >
> > > Sincerely,
> > > Xiaoxiong
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Seung's lab, 46-5065
> > Department of Brain and Cognitive Sciences
> > Massachusetts Institute of Technology
> > 43 Vassar St.
> > Cambridge, MA 02139
> > USA
> >
> > Phone: [phone]
> > Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html