Open Microscopy Environment

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

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

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);

maringa wrote: 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.

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.

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.