installed a good quality cam for the Pi and calibrated the position. tricky to set the raspistill shutter speed without automatic lightening measurement. let's hope the date-time is always picked up from the wifi if I leave that on. The I2C that would hold the RTC is blocked by the servo board.
A circle-hough-transform plugin for ImageJ detects the circular markers. I should put them directly on the glass slide, so that if the slide or the box it rests on move, the image cropping can still be correctly performed.