microfluidic image stack processing
NOTE: Pre-alpha tools, functionality subject to change without notice!
Some miscellaneous tools helpful for working with image stacks (with microfluidic structures). Currently contains the following utilities:
Registration routine from molyso, will automatically register the input stack and possible additional channels.
> python -m mfisp.registration --output result.tif --channel 0 input.tifAutomatic rotation detection and de-rotation from molyso. (Hint: Try to have OpenCV installed for your Python version, otherwise the rotation will be very slow. Windows users take a look here.)
> python -m mfisp.autorotate --output result.tif --channel 0 input.tifUses the register and autorotate functionality as described above, and detects rectangular growth structures as region of interst (ROI). The resulting stack will contain only the ROI.
> python -m mfisp.boxcrop --output result.tif --channel 0 input.tif2-clause BSD.