ImageJ

IJ_Ed problem

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Daniel James White

IJ_Ed problem

Hi Kinata

for a nice dev environment for scripting etc.
try the script editor in the Fiji distro of imageJ from

http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)

it does macro lang, as well as other nice scripting languages like
javascript and python

Dan

Begin forwarded message:

> Date: Sat, 20 Mar 2010 22:51:04 -0700
> From: Kinata <[hidden email]>
> Subject: IJ_Ed problem
>
> I've been looking for a good macro editor IDE to use with IJ from
> Jérôme
> Mutterer,
> and have installed (first) JEdit and (second) the IJ_Ed package.
>
> Problem:
> -- Start IJ.
> -- Choose the new menu item Plugins>Editor>IJ Ed.
> -- The JEdit splash screen appears, but stops at "run startup
> scripts". The
> wheel spins indefinitely.
> -- Quit IJ.
>
> I see on the IJ_Ed page at imagejdocu.tudor.lu that it's good to
> edit the
> ImageJ.cfg file, but it didn't
> seem necessary, as the menu item appeared. Here's mine:
>
> .
> C:\Program Files\Java\jdk1.6.0_18\bin\javaw.exe
> -Xmx1200m -cp C:\PROGRA~1\Java\JDK16~1.0_1\lib\tools.jar;ij.jar
> ij.ImageJ
>
>
> As an aside, can anyone recommend a good IDE for IJ that runs under
> Windows?

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net BioImageXD
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

David Holtzclaw

Reading PICT files

Good afternoon!

I'm trying to read *.PICT files into ImageJ version 1.43g using the File -
import - *.pict command or the Jimi Reader pluggin and I am unsuccessful
either way. I get the following error:

"java.lang.IllegalStateException: Error loading image."

Any help would be greatly appreciated.

Thanks
David

David Holtzclaw, Ph.D.
DRC 6012
Cellular & Integrative Physiology
985850 Nebraska Medical Center
Omaha, NE 68198-5850
(402) 559-6013 (voice)
(402) 559-4438 (Fax)
Email: [hidden email]

University of Nebraska Medical Center E-mail Confidentiality Disclaimer:
The information in this e-mail may be privileged and confidential,
intended only for the use of the addressee(s) above. Any unauthorized use
or disclosure of this information may be prohibited. If you have received
this e-mail by mistake, please delete it and immediately contact the
sender.

David Holtzclaw

12-bit images

In reply to this post by Daniel James White

On the listserv, I've seen a few previous postings asking how to get
ImageJ to read 12-bit images, but I've been unable to find any answers. Is
there a way to get ImageJ to read 12-bit grayscale images without just
converting them to either 8-bit or 16-bit images?

Thanks
David

David Holtzclaw, Ph.D.
DRC 6012
Cellular & Integrative Physiology
985850 Nebraska Medical Center
Omaha, NE 68198-5850
(402) 559-6013 (voice)
(402) 559-4438 (Fax)
Email: [hidden email]

University of Nebraska Medical Center E-mail Confidentiality Disclaimer:
The information in this e-mail may be privileged and confidential,
intended only for the use of the addressee(s) above. Any unauthorized use
or disclosure of this information may be prohibited. If you have received
this e-mail by mistake, please delete it and immediately contact the
sender.

ctrueden

Re: 12-bit images

Hi David,

ImageJ and Bio-Formats read a variety of 12-bit image formats into ImageJ by
loading them as 16-bit, which retains the full intensity range possible with
12-bit data (0-4095).

-Curtis

On Mon, Mar 22, 2010 at 7:37 PM, David Holtzclaw <[hidden email]>wrote:

> On the listserv, I've seen a few previous postings asking how to get
> ImageJ to read 12-bit images, but I've been unable to find any answers. Is
> there a way to get ImageJ to read 12-bit grayscale images without just
> converting them to either 8-bit or 16-bit images?
>
> Thanks
> David
>
> David Holtzclaw, Ph.D.
> DRC 6012
> Cellular & Integrative Physiology
> 985850 Nebraska Medical Center
> Omaha, NE 68198-5850
> (402) 559-6013 (voice)
> (402) 559-4438 (Fax)
> Email: [hidden email]
>
> University of Nebraska Medical Center E-mail Confidentiality Disclaimer:
> The information in this e-mail may be privileged and confidential,
> intended only for the use of the addressee(s) above. Any unauthorized use
> or disclosure of this information may be prohibited. If you have received
> this e-mail by mistake, please delete it and immediately contact the
> sender.
>

ctrueden

Re: Reading PICT files

In reply to this post by David Holtzclaw

Hi David,

Bio-Formats can read PICT files: http://loci.wisc.edu/bio-formats/imagej

-Curtis

On Mon, Mar 22, 2010 at 7:34 PM, David Holtzclaw <[hidden email]>wrote:

> Good afternoon!
>
> I'm trying to read *.PICT files into ImageJ version 1.43g using the File -
> import - *.pict command or the Jimi Reader pluggin and I am unsuccessful
> either way. I get the following error:
>
> "java.lang.IllegalStateException: Error loading image."
>
> Any help would be greatly appreciated.
>
> Thanks
> David
>
>
> David Holtzclaw, Ph.D.
> DRC 6012
> Cellular & Integrative Physiology
> 985850 Nebraska Medical Center
> Omaha, NE 68198-5850
> (402) 559-6013 (voice)
> (402) 559-4438 (Fax)
> Email: [hidden email]
>
> University of Nebraska Medical Center E-mail Confidentiality Disclaimer:
> The information in this e-mail may be privileged and confidential,
> intended only for the use of the addressee(s) above. Any unauthorized use
> or disclosure of this information may be prohibited. If you have received
> this e-mail by mistake, please delete it and immediately contact the
> sender.
>

Gluender-3

Re: Reading PICT files

In reply to this post by David Holtzclaw

David,

not sure what the "Jimi Reader pluggin" is, but Apple's PICT-format
allows pixel images, vector graphics and both.

Are you sure that your PICT-files contain pixel images only?

MacOSX Preview will open PICT files and you can save them as
TIFF-files that ImageJ will open.

HTH
--

Herbie

------------------------
<http://www.gluender.de>

Daniel James White

Re: 12-bit images

In reply to this post by David Holtzclaw

Hi David,

just to make a small point more clear.

Computers have no native data structure for 12 bit images.
As far as the data files go and how the computer reads them , they are
always 16 bit.
Images from a 12 or 14 bit CCD camera just has the end bits empty (0)

So saying one converts 12 bit images to 16 bit is not the right way to
think about it.
ImageJ will always open images containing 12 bits on info as 16 bit.
Thats perfectly normal.
No info is changes or lost (like it would be if you converted to 8 bit
upon opening it)

cheers

Dan

Begin forwarded message:

>
> Date: Mon, 22 Mar 2010 13:37:51 -0500
> From: David Holtzclaw <[hidden email]>
> Subject: 12-bit images
>
> On the listserv, I've seen a few previous postings asking how to get
> ImageJ to read 12-bit images, but I've been unable to find any
> answers. Is
> there a way to get ImageJ to read 12-bit grayscale images without just
> converting them to either 8-bit or 16-bit images?
>
> Thanks
> David
>
> David Holtzclaw, Ph.D.
> DRC 6012
> Cellular & Integrative Physiology
> 985850 Nebraska Medical Center
> Omaha, NE 68198-5850
> (402) 559-6013 (voice)
> (402) 559-4438 (Fax)
> Email: [hidden email]