[OpenSPIM] defining interest points fails

Dr S. Hoehn S.Hoehn at damtp.cam.ac.uk
Mon Jun 6 11:02:09 CDT 2016


Dear All,

Has anyone recently had trouble with the registration of multi-view SPIM
data? If you encountered the problem described below I'll write a bug
report, but I first wanted to know if I'm just forgetting something:

I have been trying to register z-stacks from 3 angles at a single time
point with the old fiji plugin (SPIM Registration) and the new one
(Multiview Reconstruction). In each case when I try to choose a z-stack
for finding interest points I get the following error message:

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51a; Java 1.6.0_24 [64-bit]; Windows
7 6.1; 428MB of 490870MB (<1%)

java.lang.IllegalArgumentException: STACK IS EMPTY
     at ij.ImagePlus.setStack(ImagePlus.java:642)
     at ij.ImagePlus.<init>(ImagePlus.java:149)
     at
net.imglib2.img.display.imagej.ImageJFunctions.makeImagePlus(ImageJFunctions.java:245)
     at
net.imglib2.img.display.imagej.ImageJFunctions.wrapFloat(ImageJFunctions.java:240)
     at
spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian.setInteractiveValues(DifferenceOfGaussian.java:238)
     at
spim.fiji.plugin.interestpointdetection.DifferenceOf.queryParameters(DifferenceOf.java:225)
     at
spim.fiji.plugin.Interest_Point_Detection.detectInterestPoints(Interest_Point_Detection.java:161)
     at
spim.fiji.plugin.Interest_Point_Detection.run(Interest_Point_Detection.java:67)
     at ij.IJ.runUserPlugIn(IJ.java:216)
     at ij.IJ.runPlugIn(IJ.java:180)
     at ij.Executer.runCommand(Executer.java:137)
     at ij.Executer.run(Executer.java:66)
     at java.lang.Thread.run(Thread.java:662)

I attached the z-stacks I wanted to register and fuse (as Google Drive
links, below). I chose the first one to find beads.​
  spim_TL01_Angle2.tif [1]​​
  spim_TL01_Angle0.tif [2]​​
  spim_TL01_Angle1.tif [3]​

With the old SPIM Registration a window opens showing the first image of
the stack (instead of the entire z-stack) and it doesn't show any green
or red circles around beads, no matter where I set the threshold.

Would anyone have any ideas what's going wrong?

Thanks a lot!

Best wishes,
Stephanie

-- 

Stephanie Hoehn
DAMTP, Biological Physics
Centre for Mathematical Sciences
Wilberforce Road
Cambridge
CB3 0WA
United Kingdom
OFFICE TEL: 01223 337859
Office: H0.03

-- 

Stephanie Hoehn
DAMTP, Biological Physics
Centre for Mathematical Sciences
Wilberforce Road
Cambridge
CB3 0WA
United Kingdom
OFFICE TEL: 01223 337859
Office: H0.03

Links:
------
[1] 
https://drive.google.com/file/d/0B7_ptH2Tf_XdcEowRDJncF9mekE/view?usp=drive_web
[2] 
https://drive.google.com/file/d/0B7_ptH2Tf_XdazFFRlBYSXp5YzA/view?usp=drive_web
[3] 
https://drive.google.com/file/d/0B7_ptH2Tf_XdWkV2cGtGQU1yUDQ/view?usp=drive_web




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