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Task #12584 (new)

Opened 5 years ago

Last modified 4 years ago

Add support for .oct files

Reported by: mlinkert Owned by:
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: 5.0.5
Keywords: new-format, external Cc: sauer.benjamin@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See file in QA 9562. The .oct file is a Zip file that contains a directory of spectral data files (one per channel?) and a top-level XML file describing the data files. The .data files appear to be raw pixels.

It's not completely clear to me what the original acquisition system was (the only indication is "Hyperion_V1" in the Header.xml, but there are multiple possible candidates).

Change History (2)

comment:1 Changed 5 years ago by mlinkert

Additional information from private email:

So the recording device was a modified Hyperion OCT from Thorlabs. The System is discontinued but the software is used in the onfollowing systems like Telesto. The files .oct are zip container with the xml for metadata and data files. The specialty is, that it can contain processed and unprocessed data. The raw formate are as you have seen spectral information. It’s from an oct system so what is saved there are the interferograms for a so called b-scan which is a linesman of the sample. Spectra contains all the information for a b-scan. It’s unprocessed data so no picture in the regular way. The software can save raw and or processed information. The processed data is a classical „picture“! combined of the processed b-scans, either in time or space or both, this should be described in the xml file. For an imageJ plugin probably only the processed data are of interest. But for OMERO also the original data might be interesting to save. Combined with a matlab processing routine one might be able to test several processing alternatives while using the data from the server as source.

comment:2 Changed 4 years ago by mlinkert

  • Keywords external added
  • Owner mlinkert deleted

I haven't yet found a way to get Thorlabs' OCT software, but the manual looks to be somewhat useful: https://www.thorlabs.com/thorcat/21200/HYPERION-SoftwareManual.pdf

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