Bug 1066 – Analyze particles works on a two-color composite but not on a single image

Bug 1066 - Analyze particles works on a two-color composite but not on a single image


Summary:	Analyze particles works on a two-color composite but not on a single image

Status:	NEW

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-05-08 12:55 CDT by jcf14
Modified:	2015-05-08 13:06 CDT
CC List:	1 user (show)

See Also:

Attachments
This is the thresholded single color image. (85.35 KB, image/tiff) 2015-05-08 13:02 CDT, jcf14
Thresholded two-color image. (341.94 KB, image/tiff) 2015-05-08 13:06 CDT, jcf14

Description jcf14 2015-05-08 12:55:32 CDT

I am using "Analyze particles" to create ROIs on an auto-thresholded image (I will try to upload the image).  It works well when the image is a two-color composite (but just thresholding and analyzing particles in one color).  However, if I split the two-color composite into individual single-color images, the same exact process yields only one ROI, and the ROI is the size of the entire image.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-10M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/ImageJ/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150501144914)
Fiji: http://fiji.sc/update/ (last check:20150507160342)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150427062945)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150507212642)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150302170629)

Files not up-to-date:
  5ffb7d0f (OBSOLETE_UNINSTALLED) 20150413112913 jars/bio-formats/ome-jxr.jar
  d2af3ac9 (OBSOLETE_UNINSTALLED) 20150319162909 jars/kryo-2.21-shaded.jar

Comment 1 jcf14 2015-05-08 13:02:52 CDT

Created attachment 250
This is the thresholded single color image.

This is the image that, when I run "Analyze particles", it returns a single large ROI equal to the whole image.

Comment 2 jcf14 2015-05-08 13:06:29 CDT

Created attachment 251
Thresholded two-color image.

Analyzing particles in the green channel works fine in this image.

I've just realized that this is a 16-bit image, whereas for some reason the threshold process converted the single-color image into an 8-bit image. I'm not sure why it would do this or if this is the reason for the issue.