Opening POIR Olympus files

Hello!
I’m trying to open a batch of poir files delivered by an Olympus LEXT OLS 5000 laser scanning confocal microscope (poir = packed oir, as far as I know).
I can load them with the OlympusViewer plugin, but I need to process lots of them and I cannot figure out how to automatize it (the macro recorder does not produce anything useful).
Bio-Formats seems to open oir files, but not poir. Does anyone already had the same problem?
Thank you,

Nicolas

Hi @Nicolas,

sorry for the delay in answering. From the Bio-Formats perspective, this is the first time we hear about data stored using the POIR format. From what you describe, it looks like the data structure is different enough from the OIR file format so that the reader cannot read it.

Initial support for the OIR file format had been introduced in partnership with Olympus Europe in 2017. Since then, many breaking variants of the file format have been reported by the community - see
OME’s position regarding file formats. Unfortunately, this very much feels like the same issue.

As usual in these situations (see Opening .lof Leica files), have you been in touch with contact with Olympus and asked them if there are any plans to ensure this file format is supported for the bioimaging community in a manner that does not exclusively rely on academically funding project?

Best,
Sebastien

1 Like

Hi @Sebastien,

No problem. Thank you for the links. I totally understand and agree with OME’s position. It should be Olympus’ work to provide open or at least freely accessible readers for their new formats. We’re in contact with our vendor here (North America) for trying to find a solution. I’m afraid it’s going to take time.
Thank you for your support.

Nicolas

2 Likes