Mvd2 issues on fiji

Hi trying to open an mvd2 file generated from velocity through FIJI. Had no issues opening this file with bioformats from previous testing last year, but this time round it’s not managing to open the mvd2. This is the error I am getting:

"(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 35MB of 2934MB (1%)

java.lang.IllegalArgumentException: Invalid series: 0
at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1253)
at loci.formats.FormatReader.setSeries(FormatReader.java:934)
at loci.formats.in.VolocityReader.initFile(VolocityReader.java:691)
at loci.formats.FormatReader.setId(FormatReader.java:1395)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:229)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.IJ.runPlugIn(IJ.java:182)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:229)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.IJ.runPlugIn(IJ.java:182)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:516)
at ij.io.Opener.openImage(Opener.java:370)
at ij.io.Opener.openImage(Opener.java:242)
at ij.io.Opener.open(Opener.java:109)
at ij.io.Opener.openAndAddToRecent(Opener.java:291)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
at java.lang.Thread.run(Thread.java:745)

Does anyone know how to handle this?

Cher

Hi @cfarrugia, if you are able to upload the sample file for testing to https://www.openmicroscopy.org/qa2/qa/upload/ that would be a great help.

Is it the exact same file which had previously opened ok?
Do you happen to remember what version of Bio-Formats or the rough timeframe when it was working last?

Hi @dgault. Thanks, just uploaded the file. Tried opening the other file I was using last year ending with mvd2 as well and had no issues, but still having issues with this one for some reason. Tried updating my fiji but anyway not reading it. Attached pic of bioformats version I am currently using, which still works for the older mvd2 files I have.

Could the size of the file be an issue? This file should be larger than the older one and also has videos.

BW,
Cher

Thanks @cfarrugia for uploading the file. I was able to test it and the issue appears to be that it is unable to locate the rest of the dataset which should be a number of atsf, aisf and aiix files in a folder called Data. Do you know if these files are missing or located in the wrong place perhaps?

Hi @dgault. Yes I also have those file in a folder called data which is located in the same file in my devices (didn’t upload those files on omero though). Should I upload the atsf etc on omero as well? In the mean time I’ll try reuploading the data files from the microscope hard disk just in case something went wrong during the upload from the microscope computer to my google drive and external hard drive.

Hi @cfarrugia, sorry for the delayed response as I have been off for a number of days. You will need to upload all of the files in the data folder as well.

Hi. Thanks for your help. Tried to reupload the files and it finally opened without issues, so something must have gone wrong during the upload or download from/to google drive.
BW,
Cher