Comments (3)
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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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 theOifFile.mainfile
attribute. You can also convert OIB to OIF with theoib2oif
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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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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