Components of the system

The system is built on a stereomicroscope (Leica S9i, Germany) with a large working distance to fit the pipette between the sample and the objective. This microscope has an integrated 10MP CMOS camera directly connected to the controller PC via USB port. The motorized stage (Marzhauser, Germany) has a 100 × 150 mm movement area. We designed a 3D printed plate holder that is compatible with the most common microwell plates, including 24-, 96-, or 384-well plates (Fig. 3c,d). A two-axis micromanipulator is installed next to the microscope and can be controlled at a micrometer precision. A custom-designed stepper motor-driven syringe pump ensures high precision (3 µl) fluid movement. The whole system is small, thus mobile, and can be installed under a sterile hood.

(a) SpheroidPicker prototype. The main components are shown, which are the manipulator, the syringe pump, and a stereo microscope. (b) The 3D printed element that fixes the capillary holder to the linear actuators. (c) 3D model of the custom-made plate-mounting system that is compatible with the most common 24-, 96-, 384-well plates. The source and target plate can be placed next to each other. (d) Model of a petri dish holder which can be inserted into the 96 -well plate holder.

The software performs four major operational steps (1) entire hardware control, (2) automated imaging, (3) spheroid detection using a trained Mask R-CNN¹⁵ deep learning framework (described later), and (4) an easy to use graphical user interface to define custom spheroid selection and transfer criteria.