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Micromanager/Fiji errors

PostPosted: Sat Feb 01, 2014 5:01 pm
by daknecht
I have encountered 2 bugs (I think) in BioFormats (Mac/mavericks/Fiji):

1. If you collect a dataset with Micro-manager, (1.4.15) and stop the collection early, Bioformats will open a stack of the originally designated number of files (not the actual) and all will be blank (zero at all pixels). The same folder opened by Import/Image Sequence will open just fine.

2. When I try to export from Fiji as a Quicktime movie, I get the following error message:

loci.formats.FormatException: Unsupported image type 'uint16'.
at loci.formats.FormatWriter.checkParams(
at loci.formats.out.QTWriter.saveBytes(
at loci.formats.FormatWriter.saveBytes(
at ij.plugin.filter.PlugInFilterRunner.processOneImage(
at ij.plugin.filter.PlugInFilterRunner.<init>(
at ij.IJ.runUserPlugIn(
at ij.IJ.runPlugIn(
at ij.Executer.runCommand(

Re: Micromanager/Fiji errors

PostPosted: Mon Feb 03, 2014 10:17 am
by wmoore

1. Please could you send us a sample dataset so we can reproduce this. You can upload data at - Probably best if you zip up your dataset into a single zip file for upload.

2. You need to convert images to "8 bit" data before you export to Quicktime. In the ImageJ menu, go to Image -> Type -> 8 bit. After this conversion, the export should work fine.



Re: Micromanager/Fiji errors

PostPosted: Mon Feb 03, 2014 5:46 pm
by daknecht
Hi- Just uploaded a dataset that should show this behavior. It was one I sent to Melissa a while back but did not get a response. If it does not work, let me know as I have others. Will play with QT later. Dave

Re: Micromanager/Fiji errors

PostPosted: Mon Feb 03, 2014 7:03 pm
by daknecht
I tried the 8 bit quicktime export and it worked, but I cannot see any way to choose a codec. The movie that was exported was uncompressed and I never got a dialog to choose a codec.

Re: Micromanager/Fiji errors

PostPosted: Fri Feb 07, 2014 1:59 pm
by rleigh
The QuickTime writer (QTWriter) does have an option to set the codec (setCodec()), but this does not appear to be made available to you via the ImageJ Plugin interface. So the functionality you want is present, but not directly accessible via the user interface.

I opened a ticket for this: and added you as a CC so you will be notified on any changes.


Re: Micromanager/Fiji errors

PostPosted: Tue Feb 11, 2014 12:32 am
by mlinkert
My apologies for not following up on the Micromanager issue sooner. There is now a ticket for it on our issue tracking system:

You have been CC'd, and so will be notified of our progress. If you would prefer not to receive automatic updates, please let us know.