Cell colony picking system

An apparatus for picking cell colonies, comprising:

• an apparatus bed configured to receive a sample container, wherein the sample container comprises a transparent base supporting a volume of semi-solid medium in which a plurality of cells is present;
• a digital camera having an objective disposed below the apparatus bed, such that digital images of the cells in the semi-solid medium are capturable through the transparent base of the sample container;
• a Z-axis positioner coupled to the objective and configured to position the objective at a selectable vertical height;
• a picking head of the apparatus to isolate at least a portion of a cell colony;
• and
• a controller coupled to the digital camera, the Z-axis positioner, and the picking head, the controller having a processor configured to execute a stored set of instructions
• (i) to capture at a first time and using the digital camera a first plurality of vertically spaced-apart images of the volume of semi-solid medium, each image taken through the transparent base and having a different height along the Z axis, such that a first volumetric image stack is generated;
• (ii) to identify based on one or more images of the volume of semi-solid medium captured at a second time substantially later than the first time, a location of one or more candidate colonies of cells;
• (iii) to determine based on the volumetric image stack, a measure of likelihood, for each candidate colony, that the candidate colony is monoclonal, wherein the determine step comprises:
• to correlate the position of the one or more candidate colonies in the one or more images captured at the second time with the position of a single cell in the images captured at the first time;
• to identify, from the plurality of single cell locations, single cells that are spaced from all other cells by at least a selected first distance;
• and
• to limit potential locations of each candidate colony of cells to locations corresponding to the identified single cells;
• (iv) to compile a pick list of colony coordinates using the measure of likelihood that a colony is monoclonal;
• and
• (v) to position the picking head to isolate at least a portion of the colonies of the pick list.