Welcome to Camera Stage Mapping’s documentation!
This Python module allows you to calibrate a microscope’s stage against the camera. By moving the sample a known number of steps, and tracking how far the image translates, it is possible to recover the number of steps per pixel. This code goes a step further, and recovers a 2x2 affine transformation matrix, so it will cope with rotation, flipping, and non-uniform scaling of the X and Y axes. The calibration routines are designed to be relatively robust and minimally parameterised, so they start by determining a sensible step size automatically.
The main calibration routine is calibrate_backlash_1d()
which operates in 1D, but can be run twice in orthogonal directions and
then combined with image_to_stage_displacement_from_1d().
This is more robust than the 2D grid calibration method. Both of these
functions are defined in camera_stage_calibration_1d
The underlying cross-correlation tracking code can be configured to use
either FFT or direct correlation (FFT is recommended), and the details
are in fft_image_tracking or correlation_image_tracking.
Most of the legwork of keeping track of stage and camera coordinates is
done by camera_stage_tracker.Tracker.
Installing
This package is managed using poetry and can be installed by cloning the repository and running poetry install. It is not yet distributed on PyPI, though that’s our long term plan.
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