LIF reader

[Glen MacDonald-2]

Hello,
Does anyone have a plugin or macro that will read the Leica LIF format?  LOCI-tools 4.1.1, 12-3-09 and the current trunk build 6537 are throwing exceptions.  
Mac OSX10.6.3, ImageJ 1.44c.

Thanks,
Glen


Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

[Jason Swedlow]

Hi Glen-

Can you upload the offending data to the bio-formats site you have?
This is one of those 'works for us' things, so we need to see the
specific data.

Thanks!

Cheers,

Jason

On 19/06/2010, Glen MacDonald <[hidden email]> wrote:

> Hello,
> Does anyone have a plugin or macro that will read the Leica LIF format?
> LOCI-tools 4.1.1, 12-3-09 and the current trunk build 6537 are throwing
> exceptions.
> Mac OSX10.6.3, ImageJ 1.44c.
>
> Thanks,
> Glen
>
>
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> Box 357923
> University of Washington
> Seattle, WA 98195-7923  USA
> [phone]
> [hidden email]
>

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
Open Microscopy Environment: http://openmicroscopy.org
**************************

[Glen MacDonald-2]

Installing the HandleExtraFileTypes plugin allowed use of  drag and drop to work with LIF.  Now calling the plugin from the menu also works with LIF and Olympus OIB.

Glen

On Jun 19, 2010, at 8:09 AM, Glen MacDonald wrote:

> Hello,
> Does anyone have a plugin or macro that will read the Leica LIF format?  LOCI-tools 4.1.1, 12-3-09 and the current trunk build 6537 are throwing exceptions.  
> Mac OSX10.6.3, ImageJ 1.44c.
>
> Thanks,
> Glen
>
>
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center
> Box 357923
> University of Washington
> Seattle, WA 98195-7923  USA
> [phone]
> [hidden email]

[W. Chan]

Hi Glen

This is interesting to find that HandleExtraFileTypes resolve the LIF
reading problem.  Last month, one of our users on a Mac was getting this
error with a then current trunk build.

"java.lang.IndexOutOfBoundsException: Index: 1, Size: 0"

I gave her an older working jar on my machine which is rev 5770, built
4 Jan 2010 and that has been working fine for her since.  I'll check her
plugins if the problem comes up again.  Thanks for the heads up.

On Sat, 19 Jun 2010, Glen MacDonald wrote:

> Installing the HandleExtraFileTypes plugin allowed use of drag and drop
> to work with LIF.  Now calling the plugin from the menu also works with
> LIF and Olympus OIB.
>
> Glen
>
> On Jun 19, 2010, at 8:09 AM, Glen MacDonald wrote:
>
> > Hello,
> > Does anyone have a plugin or macro that will read the Leica LIF format?  LOCI-tools 4.1.1, 12-3-09 and the current trunk build 6537 are throwing exceptions.
> > Mac OSX10.6.3, ImageJ 1.44c.
> >
> > Thanks,
> > Glen

--
Pang (Wai Pang Chan, [hidden email], PAB A087, 206-685-1519)
The Biology Imaging Facility (http://depts.washington.edu/if/)

[Glen MacDonald-2]

Thanks for the offer Jason.  
Will do it later today when I get on a decent network.  I'm at the UBC course.  Some of the vendors try to be 'helpful' and export student images as 8-bit TIFF.   I want to make sure everyone can open original formats with full bit-depth.  

Glen


On Jun 19, 2010, at 8:34 AM, Jason Swedlow wrote:

> Hi Glen-
>
> Can you upload the offending data to the bio-formats site you have?
> This is one of those 'works for us' things, so we need to see the
> specific data.
>
> Thanks!
>
> Cheers,
>
> Jason
>
> On 19/06/2010, Glen MacDonald <[hidden email]> wrote:
>> Hello,
>> Does anyone have a plugin or macro that will read the Leica LIF format?
>> LOCI-tools 4.1.1, 12-3-09 and the current trunk build 6537 are throwing
>> exceptions.
>> Mac OSX10.6.3, ImageJ 1.44c.
>>
>> Thanks,
>> Glen
>>
>>
>> Glen MacDonald
>> Core for Communication Research
>> Virginia Merrill Bloedel Hearing Research Center
>> Box 357923
>> University of Washington
>> Seattle, WA 98195-7923  USA
>> [phone]
>> [hidden email]
>>
>
>
> --
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone [phone]
> Intl phone:  [phone]
> FAX   [phone]
> email: [hidden email]
>
> Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
> Open Microscopy Environment: http://openmicroscopy.org
> **************************

[Paul Dufouleur]

Hi everyone,

I have problem to get and use the results and the ROI that the function "Analyse Particles" gave me with the following line:

IJ.run(imp, "Analyze Particles...", "size=0.00-Infinity circularity=0.00-1.00 show=[Masks] display clear add");

Could someone help me to put them in an object ResultTable and ROI?

thanks a lot,

Paul Dufouleur.

     
_________________________________________________________________
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[Rasband, Wayne (NIH/NIMH) [E]]

On Jun 20, 2010, at 11:48 AM, Paul Dufouleur wrote:

> Hi everyone,
>
> I have problem to get and use the results and the ROI that the function "Analyse Particles" gave me with the following line:
>
> IJ.run(imp, "Analyze Particles...", "size=0.00-Infinity circularity=0.00-1.00 show=[Masks] display clear add");
>
> Could someone help me to put them in an object ResultTable and ROI?

You can get the ResultsTable using

   ResultsTable rt = ResultsTable.getResultsTable();

You can get a list of the ROIs using

   Overlay rois = imp.getOverlay();

if you use the show="Overlay Outlines" option that was added to the particle analyzer in ImageJ 1.44b. This works because because an Overlay is basically just a list of ROIs.

Here is an example:

   imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/blobs.gif");
   IJ.setAutoThreshold(imp, "MaxEntropy");
   IJ.run("Set Measurements...", "area mean");
   IJ.run(imp, "Analyze Particles...", "show=[Overlay Outlines] clear");
   rois = imp.getOverlay();
   rt = ResultsTable.getResultsTable();
   for (i=0; i<rois.size(); i++)
       IJ.log(i+"  "+rois.get(i)+", area="+rt.getValue("Area", i));

-wayne