Bfconvert - error in writing files from lif to ome.tiff

Error in writing ome.tiff files using the command line. I have a .lif file with several of z stacks and two channels each. I used the bfconvert- https://docs.openmicroscopy.org/bio-formats/5.7.1/users/comlinetools/conversion.html to batch convert lif files to ome.tiff files. I wanted to separate all channels and all series into separate files. One tiff file for each channel z stack.

Bf-convert could convert the first series correctly, but all the other series were corrupted.

I used the below command with respective input and output paths:
./bftools/bfconvert ‘/media/xxx/xxx/xxx_files/Project001.lif’ ‘/media/xxx/xxx/outputname_series_%s_C%c.ome.tiff’

How can i solve the files getting corrupted.
I see the below error in fiji.

I can find it in 3d as random lines (3d view in morphographx)

How can i also include the file name for the individual series from the lif file on the output file? Below is the typical lif file that we have with several series. The lif files are aquired as 12 bit images and have the voxels as in the file name.

Best Regards,
Athul

Hi @Athul_r.vijayan,
Which version of bfconvert are you using ?

Thanks for the quick reply, I am using the Version: 5.6.0 of bfconvert

Is it the last version ?

Make sure you download the latest version of bftools here:

If you can retry and tell us if the problem persists, that would be nice.

Thanks a lot, it worked. Now i could bulk export lif to tiff. I have another serious issue with the file names that are exported. How can i direct the names from the lif file as here?

What are the filenames currently ?

Maybe somebody from @OMETeam can suggest something, but I’m not sure you can change the default name given by bftools in command line.

@Athul_r.vijayan welcome to the forum. The series_%s in your initial post will expand to the series index. To use the series name instead, you should be able to switch to %n instead e.g.

$ ./bftools/bfconvert /media/xxx/xxx/xxx_files/Project001.lif /media/xxx/xxx/%n_C%c.ome.tiff’

bfconvert -h should provide a list of all available patterns in case you need more granularity.

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Very cool! Is there a web documentation for these options ? Or is bfconvert -h the best option ?

Best,

Nicolas

@NicoKiaru in terms of Web documentation, the bfconvert technical documentation page should mirror most of the options exposed by the utility help.

There are still out-of-sync bits between the two locations. For instance, not all the expansion patterns are documented. The source page of the documentation is available here if you or anyone wanted to contribute with a Pull Request. Otherwie, if we cannot get to it in time for the next patch release, we can capture this as a backlog issue.

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Thanks a lot @NicoKiaru @s.besson for all support.

The case is closed. Everything is working fine.

Best,
Athul

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