Bug 996 – Binary image

Bug 996 - Binary image


Summary:	Binary image

Status:	RESOLVED INVALID

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-01-27 23:39 CST by Kentaro Noma
Modified:	2015-02-04 16:04 CST
CC List:	3 users (show)

See Also:

Description Kentaro Noma 2015-01-27 23:39:43 CST

Dear Sir/Madam,

What I want to do is making a binary file and use it as ROI for the measurement of another file.
So,
I made a binary file (File1).
I chose the File1 for "Redirect to" in the "Set measurement" command to analyze another file (File2).
I tried to do "Particle analysis" for File2.
But it shows the following error no matter how I make a binary file:
"A thresholded file or 8-bit binary file is required. ..."
Do you have any ideas about how it happenes?

I reinstalled the latest Fiji but it did not help.
I checked the File1 is binary by extracting values.
Thanks.

Ken

Information about your version of Java:

  os.arch => amd64
  os.name => Windows NT (unknown)
  os.version => 6.2
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Kentaro\DOCUME~1\Research\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Kentaro\DOCUME~1\Research\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150122044514)
Fiji: http://fiji.sc/update/ (last check:20150127132630)

Comment 1 Wayne Rasband 2015-01-28 08:54:21 CST

You need to redirect to the second image and run the particle analyzer on the  binary image. Here is a macro example:

  run("Blobs (25K)");
  rename("image1");
  setOption("BlackBackground", true);
  run("Make Binary");
  setThreshold(255, 255);
  newImage("image2", "16-bit ramp", 256, 254, 1);
  run("Set Measurements...", "area mean min redirect=image2");
  selectWindow("image1"); // select binary image
  run("Analyze Particles...", "display clear");

Comment 2 Curtis Rueden 2015-02-04 16:04:11 CST

Thanks Wayne.

Kentaro, please reopen the issue if Wayne's suggestion does not work for you.