ImageJ

Import image sequence

‹ Previous Topic Next Topic ›
 
classic Classic list List threaded Threaded
♦
♦
 2 messages Options
Knecht, David
Reply | Threaded
Open this post in threaded view
♦
♦
|

Import image sequence

Knecht, David
I am trying to import an image sequence in Fiji (updated before running) and get the following error message.  It works fine in ImageJ2.  Dave

(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.4; 1483MB of 5817MB (25%)
 
java.lang.NullPointerException
        at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:781)
        at io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:740)
        at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
        at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
        at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
        at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
        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:808)
        at io.scif.img.ImgOpener.read(ImgOpener.java:793)
        at io.scif.img.ImgOpener.read(ImgOpener.java:793)
        at io.scif.img.ImgOpener.read(ImgOpener.java:793)
        at io.scif.img.ImgOpener.read(ImgOpener.java:775)
        at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
        at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
        at net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:430)
        at ij.plugin.FolderOpener.run(FolderOpener.java:115)
        at ij.IJ.runPlugIn(IJ.java:172)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:695)

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
Storrs, CT 06269
860-486-2200

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ctrueden
Reply | Threaded
Open this post in threaded view
♦
♦
|

Re: Import image sequence

ctrueden
Hi Dave,

> java.lang.NullPointerException
>         at
io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:781)

Thanks for the report, and for filing a bug in the issue tracker:
http://fiji.sc/bugzilla/show_bug.cgi?id=885

I confirm that this is a bug in the SCIFIO Micro-Manager file format plugin.

Anyone interested in this bug can follow the progress on the issue tracker.

Regards,
Curtis


On Thu, Aug 7, 2014 at 2:02 PM, Knecht, David <[hidden email]>
wrote:

> I am trying to import an image sequence in Fiji (updated before running)
> and get the following error message.  It works fine in ImageJ2.  Dave
>
> (Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_65 [64-bit]; Mac OS X
> 10.9.4; 1483MB of 5817MB (25%)
>
> java.lang.NullPointerException
>         at
> io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:781)
>         at
> io.scif.formats.MicromanagerFormat$Reader.openPlane(MicromanagerFormat.java:740)
>         at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
>         at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
>         at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
>         at
> io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
>         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:808)
>         at io.scif.img.ImgOpener.read(ImgOpener.java:793)
>         at io.scif.img.ImgOpener.read(ImgOpener.java:793)
>         at io.scif.img.ImgOpener.read(ImgOpener.java:793)
>         at io.scif.img.ImgOpener.read(ImgOpener.java:775)
>         at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
>         at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
>         at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
>         at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
>         at
> net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
>         at
> net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
>         at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
>         at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
>         at
> net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
>         at
> net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:430)
>         at ij.plugin.FolderOpener.run(FolderOpener.java:115)
>         at ij.IJ.runPlugIn(IJ.java:172)
>         at ij.Executer.runCommand(Executer.java:131)
>         at ij.Executer.run(Executer.java:64)
>         at java.lang.Thread.run(Thread.java:695)
>
> Dr. David Knecht
> Professor of Molecular and Cell Biology
> Core Microscopy Facility Director
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Free forum by Nabble Edit this page