Which image file formats to choose?

[tischi]

I have a CZI file that I would like to contribute.

Should I convert it? To what?

My personal opinion:

It is useful to also have commercial file formats, but only for teaching how to deal with those file formats.

Data that is of general use should be in a wide spread and easy to deal with community standard file format. I think currently there the only option is OME.TIFF?!

What do you think? ping @haesleinhuepf @RoccoDAnt @ArneS70 @biovoxxel

[biovoxxel]

I think all tools we normally use for teaching run Bio-Formats and can open those readable "standard" formats. Therefore, I think if it is not the strangest format ever, I would keep the original format (also for the sake of not messing up with the metadata. For very problematic ones, we can think about a conversion. But I am the wrong person to opinionate on which is the best format.

[ArneS70]

I agree with @biovoxxel . I also recommend to not convert image data as long as it is readable with BioFormats unless there are good reasons (e.g. pyramidal data format needed).

[tischi]

OK, I wanted to disagree and say we should support community standards, but experiments that I did today appear to have such a FRUSTRATING outcome that I indeed start to wonder whether, e.g., CZI is preferable over OME.TIFF.

I am probably overreacting right now, but I spent the last couple of days dealing with various image file format issues and I am sort of loosing the patience a little bit ;-)

[haesleinhuepf]

I recently wrote this chapter out of similar frustration. In Python it's much worse compared to Java/ImageJ btw.

And I agree with the above comments. Let's keep files in the format they come if possible.

[tischi]

Yeah, I thought that at least ImageJ and Bio-Formats would play well along together. To learn that they don't is a bit of a shocker I must say....