A mix of Python scripts I might use in my daily work. License of presented scripts. No warranty - use at your own risk.
Imspector is a microscope measurement control software originating at the MPIBPC and continued and used at AI. There is a Python connection to and from Imspector, which can be exploited to facilitate usage of Imspector.
The OBF (and MSR) file format is used within my department quite frequently. The Imspector Python connection is limited to a certain CPython version and OS system. To allow analysis everywhere I made a pure Python OBF content reader.
Hop scanning (scanning along one axis in large jumps and then repeatedly shifting the offset) to fill the gaps with finely pixelated data is interesting for some special microscopy modes.
I needed to read JXR files (in Python). Matlab does not support the file format. Pillow also does not support it.
ImageIO says that it supports JXR via the FreeImage library, however it cannot load my example image and gives an exception "No known error." instead. The exception is known (see question on StackOverflow, which refers to an imageio issue which has been closed as upstream, i.e. related to the FreeImage library).
ImageIO uses "FreeImage-3.15.1-win64.dll". The current version of FreeImage is 3.18.0. There is another FreeImage Python wrapper freeimage-py but it's 3 years old and there aren't any releases.
FreeImage itself relies on libjxr, the official JXR support library from Microsoft. libjxr resided on codeplex (which will shutdown soon), copies are available on Github here and here (with a Java wrapper for BioFormats, so ImageJ/Fiji might be able to read my JXR files via BioFormats).
However, my version of Fiji (1.53c) with BioFormats (6.6.1) could not import the JXR file (UnknownFormatException).
So I give up for the moment. One could still do:
- check that the JXR file I have is a valid one with some conversion tool (like the official JxrDecApp (make JxrDecApp))
- debug ImageIO
- debug FreeImage
- debug jxrlib