Productive use of AI in bioresearch, still in its early stages, took a step forward last week with the release the Allen Integrated Cell – a predictive 3D model of the human induced pluripotent stem cell.

“Nearly every biologist has mental models of whole cells that are pieced together over their careers with information from dozens of different types of data,” said Graham Johnson, computational biologist and medical illustrator at the Allen Institute in the announcing press release. “The Allen Integrated Cell provides a new option, where 3-D visualizations of whole living cells link to analysis tools to allow for more direct data-driven exploration and hypothesis generation.”

In developing the model, the images of tens of thousands of live human stem cells were studied. Some of the cells had been genetically altered to make visible internal structures such as mitochondria. Others were unaltered cells, viewed through a standard laboratory microscope:

• First, researchers developed a computer algorithm that studied the shape of the plasma membrane, the nucleus and other fluorescently labeled cell structures to learn their spatial relationships. A powerful probabilistic model emerged from this training, that accurately predicts the most probable shape and location of structures in any cell, based solely on the shape of the plasma membrane and the nucleus.
• Second, researchers took images of those same fluorescently labeled cells and applied a different machine learning algorithm. This algorithm used what it learned from cells with fluorescent labels to find cellular structures in cells without fluorescent labels. This label-free model can be used on relatively easy to collect brightfield microscope images to visualize the integration of many structures inside of cells, simultaneously and with high precision. Viewed side-by-side, the images generated by the label-free method look nearly identical to the fluorescently labeled photographs of cells.

The new model should enable researchers to more easily and rapidly explore cells using traditional brightfield microscopy images. As noted by its developers, “The visualization shows the many molecular machines and structures (organelles) inside the cell, simultaneously. This integrated organization drives the cell’s basic functions, and these models provide a baseline for new models of different cell types, disease, drug responses, and cellular environments.”

Link to release: https://www.prnewswire.com/news-releases/allen-integrated-cell-released-online-300645289.html

Link to Allen Institute Cell Explorer: http://www.allencell.org/allen-integrated-cell.html