BF command line tools // problem splitting Volocity series
Posted: Tue Dec 18, 2012 2:18 pmDear all,
we're experiencing problems using Bio-Formats to convert a Volocity (.mvd2) container to OME-TIFF.
We used the command line tools to extract single series into separate files per timepoint. Separating timepoints was done for multiple reasons, e.g. the whole series has an overall size of ~25GB, which would make the usage of BigTIFF necessary, which then again doesn't work properly with some of our other tools (Imaris, ...). On top of that, of course speed also matters and already opening all timepoints of the series for instance in FiJi takes more than half an hour. So separating timepoints was the way to go:
After converting the series, we end up with 210 individual files, each about 120 MB in size (as expected). As explained above, opening them with FiJi takes ages (even though everything is on very fast local SSD drives), so we'd like to open the timepoints individually (for example to figure out where the interesting part happens). However, we didn't manage to do so. The Bio-Formats reader in FiJi always wants to read the whole series, no matter what options we chose in the dialog. Moving one of the individual files to a separate directory and then opening it with FiJi results in the following error message:
Trying to read one of the timepoint.ome.tif files with Imaris gives us completely strange results with messed up z-information, channels and basically everything. So we can't use Imaris as a workaround either.
Being very desperate, I even tried Huygens Essential (the free version can be used as a converter for certain formats), but it complains about being unable to increase the image memory to ~48GB. So it clearly wants to open the full timeseries as well (even though there is just one file in the directory, and no matter which one of the series).
Any help is very much appreciated!
~Niko
we're experiencing problems using Bio-Formats to convert a Volocity (.mvd2) container to OME-TIFF.
We used the command line tools to extract single series into separate files per timepoint. Separating timepoints was done for multiple reasons, e.g. the whole series has an overall size of ~25GB, which would make the usage of BigTIFF necessary, which then again doesn't work properly with some of our other tools (Imaris, ...). On top of that, of course speed also matters and already opening all timepoints of the series for instance in FiJi takes more than half an hour. So separating timepoints was the way to go:
- Code: Select all
bfconvert -bigtiff -no-upgrade -series 35 infile.mvd2 outfile_series-%s.ome.tif
After converting the series, we end up with 210 individual files, each about 120 MB in size (as expected). As explained above, opening them with FiJi takes ages (even though everything is on very fast local SSD drives), so we'd like to open the timepoints individually (for example to figure out where the interesting part happens). However, we didn't manage to do so. The Bio-Formats reader in FiJi always wants to read the whole series, no matter what options we chose in the dialog. Moving one of the individual files to a separate directory and then opening it with FiJi results in the following error message:
- Code: Select all
loci.formats.FormatException: Unmatched UUID: urn:uuid:23dc5fe4-68df-4ace-95f4-9a954284d33d
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:449)
at loci.formats.FormatReader.setId(FormatReader.java:1238)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ij.Command.runPlugIn(Command.java:146)
at ij.Command.runCommand(Command.java:95)
at ij.Executer.run(Executer.java:64)
at ij.IJ.run(IJ.java:250)
at ij.macro.Functions.doRun(Functions.java:580)
at ij.macro.Functions.doFunction(Functions.java:83)
at ij.macro.Interpreter.doStatement(Interpreter.java:219)
at ij.macro.Interpreter.doStatements(Interpreter.java:207)
at ij.macro.Interpreter.run(Interpreter.java:104)
at ij.macro.Interpreter.run(Interpreter.java:74)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:105)
at ij.IJ.runMacro(IJ.java:103)
at Action_Bar.run(Action_Bar.java:800)
at java.lang.Thread.run(Thread.java:662)
Trying to read one of the timepoint.ome.tif files with Imaris gives us completely strange results with messed up z-information, channels and basically everything. So we can't use Imaris as a workaround either.
Being very desperate, I even tried Huygens Essential (the free version can be used as a converter for certain formats), but it complains about being unable to increase the image memory to ~48GB. So it clearly wants to open the full timeseries as well (even though there is just one file in the directory, and no matter which one of the series).
Any help is very much appreciated!
~Niko
- I actually used the correct "%t" (otherwise I probably wouldn't have received the 210 individual images) 