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cgohlke avatar cgohlke commented on June 17, 2024

There are many metadata files inside OIB files (oif, txt, pty, roi, lut, bmp), mostly INI style text files, which can be parsed into nested dicts with the SettingsFile class. The main settings file can be accessed via the OifFile.mainfile attribute. You can also convert OIB to OIF with the oib2oif function. In OIF all files are stored in the file system an can be accessed with a text or image viewer. Please see the examples

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LibbyLi667 avatar LibbyLi667 commented on June 17, 2024

There are many metadata files inside OIB files (oif, txt, pty, roi, lut, bmp), mostly INI style text files, which can be parsed into nested dicts with the SettingsFile class. The main settings file can be accessed via the OifFile.mainfile attribute. You can also convert OIB to OIF with the oib2oif function. In OIF all files are stored in the file system an can be accessed with a text or image viewer. Please see the examples

Thanks for the reply. I could extract the metadata now! Just one problem - I saw there are still some information (as listed below, like the Core metadata) that I couldn't see in the oif/mainfile. Any ideas how to get these?

<style> </style>
Key Value
BitsPerPixel 12
DimensionOrder XYCZT
IsInterleaved FALSE
IsRGB FALSE
LittleEndian TRUE
PixelType uint16
Series 0 Name Series 1
SizeC 2
SizeT 1
SizeX 1024
SizeY 1024
SizeZ 1
AS Level 9999
AbsPositionUnitName mm
AbsPositionValue 0
Adjust Outward 0
Adjust Retrun 0
AnalogPMTGain 1
Confocal ON
CountingPMTGain 0
CountingPMTOffset 1.6
CountingPMTVoltage 0
Image 0 : AnalogPMTOffset 7
Image 0 : ExcitationOutPutLevel 5
Image 0 : PMTVoltage 596
Image 1 : AnalogPMTOffset 6
Image 1 : ExcitationOutPutLevel 0.5
Image 1 : PMTVoltage 657
LightControl 9999
Location Y:\MyTardisTestData\good image 02.oib
Magnification 60
Number 1
ObjectiveLens NAValue 1.35
ObjectiveLens Name UPLSAPO   60X O  NA:1.35
ObjectiveLens WDValue 9999
Observation Mode LSM
PMTDetectingMode Analog
Pan Scale 2
Path .\
Piezo AbsPositionUnitName nm
Piezo AbsPositionValue 0
PinholeDiameter 115000
PinholeScale 1
Resolution 5
RotationValue 0
RotationValue After Clip 0
RotationValue Before Clip 0
SamplingClock 250000
ScanSpeed 4
Step 0
Time Per Frame 5360256
Time Per Line 5183.999
Time Per Pixel 4
Time Per Series 32351536
X Pinhole 5
XPanValue 299
Y Pinhole -132
YPanValue -253
ZoomValue 3

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cgohlke avatar cgohlke commented on June 17, 2024

I saw there are still some information (as listed below, like the Core metadata) that I couldn't see in the oif/mainfile

Those look like properties from the OME model. You could check how Bio-Format determines them at https://github.com/ome/bioformats/blob/v6.6.1/components/formats-gpl/src/loci/formats/in/FV1000Reader.java.

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