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Author Topic: Re: Voxel image stack and then what?  (Read 708 times)
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Forums Newbie
Posts: 8

« on: March 11, 2015, 11:57:51 PM »

Hey Guys,

Was wondering if anyone here could help me out with fixing this error i get by trying to import a image sequence.

I went through the posts but couldn't find a similar problem..

so i tried a new one, the default mandelbulb without changing any preferences.

Use voxelstack, saved it in a folder on my desktop, nothing in there besides the .png's.

Tried to make an animation of it in sequimago and it works fine,

In Fiji i choose file, import, image sequence. Open the folder and the error pops up.

I work on mac, yosemite, have the latest Java installed so really don't have a clue.

I also tried changing the file names to 1.png, 2.png, 3.png..

This is the error i get.


(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.6.0_65 [64-bit]; Mac OS X 10.10; 34MB of 3333MB (1%)
java.lang.ArithmeticException: / by zero
   at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:226)
   at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
   at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:304)
   at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
   at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
   at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
   at io.scif.img.ImgOpener.read(ImgOpener.java:805)
   at io.scif.img.ImgOpener.read(ImgOpener.java:790)
   at io.scif.img.ImgOpener.read(ImgOpener.java:771)
   at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:758)
   at io.scif.img.ImgOpener.openImgs(ImgOpener.java:361)
   at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
   at io.scif.img.ImgOpener.openImgs(ImgOpener.java:146)
   at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:123)
   at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:109)
   at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
   at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
   at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
   at net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:336)
   at ij.plugin.FolderOpener.run(FolderOpener.java:114)
   at ij.IJ.runPlugIn(IJ.java:169)
   at ij.Executer.runCommand(Executer.java:131)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:695)

Fractal Molossus
Posts: 789

« Reply #1 on: March 12, 2015, 12:51:42 AM »

I don't know how to resolve the problem with Fiji, but you can also use JWildfire to create meshes from a Voxel stack, it may need more memory (not sure), but is much faster and has more options regarding this.
To do this, enter the "3DMesh Generation"-tab, and then the "Mesh generation"-tab, and press "Load sequence".
But please note that your frame-names must be in zero-padded format (e.g. "pic0001.png", ... and not "pic1.png")

Forums Newbie
Posts: 8

« Reply #2 on: March 12, 2015, 05:30:56 PM »

Thx a lot Andreas,

i'll will be trying this out tonight and let you know.

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