Reading Volocity Files

[maringa]

Is it possible to read volocity .acff files using Bioformats MatLab Package. I've tried it without success.

[sbesson]

Hi,

the Volocity ACFF files should be supported by Bio-Formats 5.0.2 and readable using the MATLAB utility functions:

Code: Select all

>> data =bfopen('Tx red.acff');
VolocityClippingReader initializing /Users/sebastien/Desktop/acff/Tx red.acff
Reading series #1
    .
>>


Can you be more specific about your unsuccessful outcome? Does the bfopen function not return at all or throw an exception? Or does the function return but the metadata/pixel data is inaccurate? Depending on the nature of your error, it may also be useful if you could send us a sample file using http://qa.openmicroscopy.org.uk/qa/upload/.

Best regards,
Sebastien

[maringa]

I can open other file formats (e.g. .ome.tiff files) but cannot open .acff files (Instead I get the error message below in matlab). I was going to upload the 'Test.acff' file but in the link http://qa.openmicroscopy.org.uk/qa/upload/ , there's no .acff option in 'Step 1: Choose file format'
>> data = bfopen('Test.ome.tiff');
Reading IFDs
Populating metadata
Reading series #1
...
>> data = bfopen('Test.acff');
Error using bfGetReader (line 80)
Java exception occurred:
java.io.EOFException: Attempting to read beyond
end of file.
at
loci.common.NIOFileHandle.readInt(NIOFileHandle.java:331)
at
loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:373)
at
loci.formats.in.VolocityClippingReader.initFile(VolocityClippingReader.java:128)
at
loci.formats.FormatReader.setId(FormatReader.java:1244)
at
loci.formats.ImageReader.setId(ImageReader.java:727)
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at
loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
Caused by:
java.nio.BufferUnderflowException
at
java.nio.Buffer.nextGetIndex(Buffer.java:478)
at
java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:336)
at
loci.common.NIOFileHandle.readInt(NIOFileHandle.java:329)
... 8 more

Error in bfopen (line 113)
r = bfGetReader(id, stitchFiles);

[jmoore]

I was going to upload the 'Test.acff' file but in the link http://qa.openmicroscopy.org.uk/qa/upload/ , there's no .acff option in 'Step 1: Choose file format'

If you could zip the file, you should be able to upload it successfully. If that's a problem, I can send you other contact info off-list.

>> data = bfopen('Test.acff');
[color=#FF0000]Error using bfGetReader (line 80)
Java exception occurred:
java.io.EOFException: Attempting to read beyond end of file.

Based on the error above, it would definitely be good to take a look at the file though.

Cheers,
~Josh.

[maringa]

Thanks Josh, I've uploaded the Test.acf.zip file . If you do successfully read it, please let me know if you can be able to get from the metadata the channels exposure times as that is what i'm looking for.

[mlinkert]

Thank you for uploading an example file. We do have a ticket for this problem on our issue tracking system:

https://trac.openmicroscopy.org.uk/ome/ticket/6413

If you would like to be automatically notified of updates to that ticket, please let us know.