Convert several timepoints and/or channels at the same time

[mbahin]

Hi,

Thanks for the nice tool.

I just discovered the -timepoint and -channel arguments. Is it possible to convert more than one timepoint at once to have a timelapse as output but not all the timepoints of the orginal .vsi file (to convert to .tif in my case)?

Cheers,
Mathieu

[dgault]

Hi @mbahin, it might be possible to simply use the range argument (https://bio-formats.readthedocs.io/en/latest/users/comlinetools/conversion.html#cmdoption-bfconvert-range). Though it is not specific to any one dimension so it may not be suitable if you have a mixture of timepoints and channels for example. In that case you might also want to combine it with the dimension swapper (https://bio-formats.readthedocs.io/en/v7.2.0/users/comlinetools/conversion.html#cmdoption-bfconvert-swap)

[mbahin]

Hi David,

Thanks for your answer!

I was actually able to do the operations I wanted to with the range argument when I have monochannel timelapse, nice!

Though, I sometimes also have timelapse multichannel files. In these files, I have, let's say, 10 timepoints for channel 1 followed by the 10 same timepoints for channel 2. I'd like to extract the timepoints, let's say, 4 and 7, for both channels. I'm not sure this is feasible using the swap argument since I didn't really get it. From what I understood, it would be to explain the program that your file is not in the expected shape dimanesions but not sure.
Could you elaborate a bit on that or point me towards a documentation with example please?

Cheers,
Mathieu