Platforms and systems for automated cell culture

A cell culture system for culturing a plurality of cells from a plurality of subjects, comprising:

• a plurality of cell samples from a plurality of subjects;
• a plurality of closed cell culture containers, each of the plurality of closed cell culture containers comprising a cell culture of a cell sample of a subject of the plurality of subjects adhered to a first surface of the closed cell culture container, the cell culture comprising a plurality of cell colonies;
• a transport mechanism configured to transport each of the plurality of closed cell culture containers between locations within the cell culture system;
• a closed liquid loop comprising a liquid handler, a fresh media reservoir, and a waste reservoir,
• wherein the liquid handler is configured to perform fluid media exchanges for each of the plurality of closed cell culture containers, and
• wherein performing the fluid media exchanges comprises (i) supplying fresh fluid media from the fresh media reservoir to each of the plurality of closed cell culture containers and (ii) pumping spent fluid media from each of the plurality of closed cell culture containers to the waste reservoir, while maintaining a closed, sterile liquid environment for the cell culture in each of the plurality of closed cell culture containers;
• a cell editing subsystem configured to selectively remove one or more cells from the first surface of each of the plurality of closed cell culture containers;
• an imaging subsystem configured to generate time-series images of the cell culture in each of the plurality of closed cell culture containers;
• and
• a computing subsystem configured to control the cell editing subsystem and to manage, in parallel, a plurality of cell culture processes being performed in the plurality of closed cell culture containers to produce a clonal induced pluripotent stem cell (iPSC) output product for each subject of the plurality of subjects, wherein the managing is based at least in part on the time-series images, and wherein managing the cell culture processes of a first cell culture container of the plurality of closed cell culture containers comprises at least one of:
• removing a first cell colony on the first surface of the first cell culture container that is predicted to collide with a second cell colony on the first surface of the first cell culture container;
• fragmenting the first cell colony into a plurality of sub-colonies;
• and
• removing at least a portion of the first cell colony to reduce a confluence or density of the first cell colony.