I've ben working on a custom STM32F405 board with better analog options in a separate project.

The key difference is the utilization of an opamp on the input, to squeeze the last bit out of the STM32F4's 12-bit ADC.

The opamp circuitry looks like this:

For reasons I don't fully understand, the opamp's input and feedback resistor values affect the output from the CCD's typical drive circuit, but changing the resistors to:

there's no clipping of the output. I guess my quantum chemistry professor was right, you can't measure a system without changing it.