Mitosis is one of the most striking things a cell does, and one of the most imaged. Despite that, it's impossible to directly image every organelle and structure going through mitosis at once. Most commonly, you see microtubules, and DNA. The Integrated Mitotic Stem Cell (IMSC) was an attempt to visualize the whole process of mitosis through the lens of every organelle.
The Allen Institute for Cell Science maintains a library of CRISPR-edited human iPS cell lines, each with one endogenous fluorescent tag: TUBA1B for microtubules, LMNB1 for the nuclear envelope, SEC61B for ER, TOMM20 for mitochondria, ST6GAL1 for Golgi, and so on through fifteen structures. Each line is a window onto one component. The IMSC project asked: what if we combined those windows into a single composite view, with each structure shown at the same moment in the cell cycle, in the same coordinate frame? The answer was a visual essay and an interactive 3D viewer — published at imsc.allencell.org — where readers can toggle channels on and off, switch between mitotic phases, and explore the integrated cell themselves.
Aligning by DNA
The technical trick was a small one with a big payoff. Each cell line was imaged in random states of the cell cycle, but every line was also DNA-stained, so we could classify each cell into one of eight mitotic phases (M0 through M7, from interphase through anaphase-cytokinesis) by the shape and texture of its DNA. Then, because DNA was a shared landmark across all the lines, we could align cells across lines by DNA position and superimpose the segmented structures phase by phase. The result is a synthesis: at each stage of mitosis you can pull up an integrated cell showing every channel in correct spatial relationship to every other channel.
We presented the work in three contexts over the course of 2019: a poster at the Gordon Research Conference on Visualization in Science & Education in the summer, a co-presentation with Chris Frink (Allen Institute) at the Allen Cell Science Symposium, and a review at the Allen Institute Scientific Advisory Board meeting. The IMSC team: Thao Do, Caroline Hookway, Gabe Medrash, Lisa Schaefbauer, Dan Toloudis, Matheus Viana, Susanne Rafelski, Graham Johnson, and me.