Bug 849 – Strange results when using the Stitching Plugin with

Bug 849 - Strange results when using the Stitching Plugin with


Summary:	Strange results when using the Stitching Plugin with

Status:	RESOLVED FIXED

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

Importance:	P5 major
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-07-10 08:47 CDT by Sebastian Rhode
Modified:	2014-08-06 10:02 CDT
CC List:	2 users (show)

See Also:

Attachments
Stitching Log Output (248.80 KB, text/plain) 2014-07-10 08:49 CDT, Sebastian Rhode
Stitching Log Output NOK (250.25 KB, text/plain) 2014-07-10 08:50 CDT, Sebastian Rhode
Stitching Result OK (Downsample Option activated) (1.20 MB, image/png) 2014-07-10 08:52 CDT, Sebastian Rhode
Stitching Result NOK (no downsampling) (1.21 MB, image/png) 2014-07-10 08:53 CDT, Sebastian Rhode
Original CZI in ZEN - RGB Image with 1 Channel (3x 8bit) (682.21 KB, image/png) 2014-07-10 08:56 CDT, Sebastian Rhode

Description Sebastian Rhode 2014-07-10 08:47:11 CDT

I tested this with the Fiji LifeLine Version 20140602.

The original CZI image can be found here:

https://dl.dropboxusercontent.com/u/623476/uncomp.czi

When I use the stitching plugin without downsampling the image, I get strange effects --> uncomp_stiched_Fiji_LifeLine.tif (3.1%).png)
Even the image still looks OK during the fusion process.

When I use the same options plus downsampling by 0.5, the result looks fine. --> uncomp_stiched_downsampled_0.5_Fiji_LifeLine.tif (6.2%).png

I also attached the Stitching Output and information about the Fiji version as TXT files.

Sebi

Comment 1 Sebastian Rhode 2014-07-10 08:49:13 CDT

Created attachment 175
Stitching Log Output

Comment 2 Sebastian Rhode 2014-07-10 08:50:54 CDT

Created attachment 176
Stitching Log Output NOK

Comment 3 Sebastian Rhode 2014-07-10 08:52:15 CDT

Created attachment 177
Stitching Result OK (Downsample Option activated)

Comment 4 Sebastian Rhode 2014-07-10 08:53:21 CDT

Created attachment 178
Stitching Result NOK (no downsampling)

Comment 5 Sebastian Rhode 2014-07-10 08:56:53 CDT

Created attachment 179
Original CZI in ZEN - RGB Image with 1 Channel (3x 8bit)

Comment 6 Sebastian Rhode 2014-07-10 08:57:44 CDT

Fiji Informarion

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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: OFFLINE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Users\m1srh\DOCUME~1\FIJI_L~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\Users\m1srh\DOCUME~1\FIJI_L~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140530153818)
Fiji: http://fiji.sc/update/ (last check:20140602042212)

Files not up-to-date:
  7f5f361d (MODIFIED) 20140624094830 jars/imagej-common-0.7.6.jar
  171d6527 (MODIFIED) 20140624094950 jars/imagej-ui-swing-0.4.7.jar
  579cc9a4 (MODIFIED) 20140624094832 jars/imagej-updater-0.3.9.jar
  dde41ab6 (MODIFIED) 20140624094824 jars/mapdb-1.0.3.jar
  1f6737d8 (MODIFIED) 20140624094950 jars/minimaven-2.1.2.jar
  4f9cde52 (MODIFIED) 20140624094812 jars/scifio-0.15.4.jar
  88e656b0 (LOCAL_ONLY) 20140624094842 jars/scifio-jai-imageio-1.1.0.jar
  4147014e (MODIFIED) 20140624094820 jars/scijava-common-2.24.0.jar
  5301d508 (MODIFIED) 20140624094952 jars/scijava-ui-awt-0.1.2.jar
  cd41f2e9 (MODIFIED) 20140624094952 jars/scijava-ui-swing-0.2.4.jar
  6ca31a68 (MODIFIED) 20140624094954 jars/scripting-java-0.2.3.jar

Comment 7 Johannes Schindelin 2014-07-22 15:24:55 CDT

This issue might be a display bug in Java. Could you try to save the .tiff and display it using another program?

Comment 8 Sebastian Rhode 2014-08-06 09:27:18 CDT

Hi Johannes,

sorry it took me a while. I was traveling testing new prototypes...

You where right, it seems to be Java display bug. When I open the stitched image e in ZEN, it looks fine. While in Fiji (and ICY) the result look similar strange.

So I close this bug.

Cheers,  Sebi

Comment 9 Johannes Schindelin 2014-08-06 10:02:15 CDT

> You where right, it seems to be Java display bug. When I open the stitched image e in ZEN, it looks fine. While in Fiji (and ICY) the result look similar strange.

Thank you for the feedback. This is actually a problem I diagnosed with the tremendous help of my colleague Yuming Liu.

If only I had unlimited time, I would know exactly what to do: enhance the ImageJ2 GUI framework to make use of OPS for zooming, and of course implement zooming in OPS (and make it *fast*). But for the moment, I have to take care of other things (some tasks unrelated to image processing, even, only to pay the bills...).

Alas, if only I had unlimited time ;-)