mesoSPIM: importer and image format

Data Management
,
#1

Hi all,

I have the same issue as @nabila.elarouci when trying to import a .raw image to omero:
the upload failed and the message is:

loci.formats.UnknownFormatException: Unknown file format: C:\Users\cstoffel\Desktop\175_647nm-350-374.raw

at loci.formats.ImageReader.getReader(ImageReader.java:202)

at loci.formats.ImageReader.setId(ImageReader.java:844)

at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.Memoizer.setId(Memoizer.java:662)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)

at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)

at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)

at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)

at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)

at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5965)

at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1113)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:127)

at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)

at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)

at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)

at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)

at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)

at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)

at java.lang.Thread.run(Thread.java:748)

at org.openmicroscopy.shoola.env.data.util.Status.update(Status.java:601)

at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)

at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:458)

at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)

at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)

at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)

at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)

at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5965)

at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1113)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)

at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:127)

at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)

at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)

at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)

at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)

at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)

at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)

at java.lang.Thread.run(Thread.java:748)

Caused by: loci.formats.UnknownFormatException: Unknown file format: C:\Users\cstoffel\Desktop\175_647nm-350-374.raw

at loci.formats.ImageReader.getReader(ImageReader.java:202)

at loci.formats.ImageReader.setId(ImageReader.java:844)

at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.Memoizer.setId(Memoizer.java:662)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)

... 16 more

So it seems that OMERO doesn’t know the .raw file format, althought this format is readible by BioFormats? Also, I am able to open the same .raw file with FIJI, with the following specifications at import:
Open_w_FIJI

Does anyone have an explanation for that?

Thank you very much,
Claire

3 Likes
Importer and image format
#2

took the liberty of editing your post to make the error message more apparent.

2 Likes
#3

Hi @stoffelc,

It should be that any file that Bio-Formats can read OMERO can read. Here you’ve opened the file in FIJI with Import > Raw.... What happens if you use Bio-Formats > Bio-Formats Importer? Do you see any error message?

~Josh

#4

Hi @joshmoore,

thank you very much for your answer.
I just tried to open it with the Bio-Formats Importer from FIJI. I get the following error message:

loci.formats.UnknownFormatException: Unknown file format: C:\Users\cstoffel\Desktop\175_647nm-350-374.raw
	at loci.formats.ImageReader.getReader(ImageReader.java:202)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:627)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
	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:235)
	at ij.IJ.runPlugIn(IJ.java:198)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)

I know that I can always save my image as an OME-tiff to import it to OMERO, but I would prefer to keep the original file format. Is there a way to make my .raw file readable by Bio-Formats? (I’ve seen that .raw are in the list of supported formats)

Claire

#5

Hi Claire,

Unfortunately, there are lots of different uses of “raw”. Can you tell us more about where this file came from or perhaps even share one with us? It’s possible for example that the codec that it is written with is not supported.

~Josh

#6

Hi Josh,

The files are volumetric images acquired with a lightsheet microscope in an imaging platform. After the acquisition, the platform staff gives us .raw files and .txt files containing the associated metadata. You can find one example file here, with the associated metadata:

Best,
Claire

1 Like
#7

Hi Claire,

thanks for the sample data. I can certainly confirm what you saw in that mesoSPIM data is not parseable by Bio-Formats. The basic solution I can offer is to follow your Import > Raw path and export to TIFF. You can see how others worked with this data under:

All the best,
~Josh

1 Like
#8

Hi Josh,

Thank you very much for your answer. I will definitely have a look to this guide!

Best,
Claire

1 Like
#9

Hi, Claire,
I am late to the party, but here is how you can open your file: Import > Raw
image
Here is what I see:

image
image2048Ă—2048 94.6 KB

Pro tip: try updating mesoSPIM control software from the development branch. It can write directly into Fiji/BigStitcher-compatible HDF5 file, which I recently implemented. This is a huge difference, especially when using multi-tile scans - all data is nicely arranged in a single H5 file, ready to be stitched.

2 Likes