Scale-free Vertical Tracking Microscopy, aka Gravity Machine
"How to track a single cell at microscale resolution while allowing free vertical movement over ecological-scales?"
Accessing micro-scale behaviors over ecological scales is a fundamental challenge since constructing a vertical water column which is even a few meters in height poses practical constraints when the desired view-point is microscopic. For the last 300 years of history of microscopy, majority of subjects of the microscopic world have been stuck under a cover slip in the X-Y plane (horizontal plane). But by definition, plankton in the ocean are very far from such confined environments, suspended in the ocean where gravity is the one constant. So how can we observe microscopic life traverse ecological length scales?
To address this challenge we invented the nearest thing we could imagine to an "endless" water-column using a simple insight "A circle has no beginning (or end)": The result is a microscope stage which functions as a "hydrodynamic treadmill" for single-cells.
The idea works as follows: An upright circular chamber with an annulus of fluid serves as our 'endless' water-column. A horizontal light-microscope focussed at either the 3 o'clock or 9 o'clock locations allows vertical movements of a cell or object to be tracked by compensatory rotation of the circular chamber such that a freely swimming cell is kept within the microscope's field-of-view. Linear tracking along the two horizontal directions allows full 3D localization of the cell. The imaging system acquires images at fast-rates and enables closed-loop 3D tracking using real-time computer vision algorithms as well as focus-tracking.
We utilize Gravity Machine to track both living and non-living objects; including in lab and field settings. This framework of long-distance, long-time scale, yet micron and millisecond resolution tracking of freely moving objects under the influence of gravity provides us a very large phase space of problems from fundamental fluid mechanics (how falling beads interact) to never before observed biological phenomena (how organisms modulate their density in real time).
"Our focus on building a general purpose instrument for tracking native behavior of freely moving micro-organisms in lab and the field, is to both bring a little piece of ocean into lab settings and also take a piece of the lab to the ocean."
To find details of how Gravity Machine works; please read our current paper in Nature Methods .
Also head over to the data gallery to discover datasets of multi-scale plankton behaviors from eight phylla across the tree-of-life.
As we charge ahead building more and more sophisticated versions of Gravity Machine, we are using this space to share our skills and insights of building this instrument and share our work openly for non-commercial, research use. We have also been developing multiple versions of Gravity Machine, some that are compatible with traditional microscopes already present in laboratories around the world and others that are better suited for operating on a research vessel at sea. In fact, we have adapted and improved many aspects of the tool as we take our instruments to the field, both at marine stations around the world and on research vessel.
Importantly, we have designed the latest version of Gravity Machine in a manner that others can follow our guide on how to replicate this work. As we finalize the latest version of code and hardware, we will freely share it online on this site for research groups replicating our work.
Although we share the current version of the code base below (both for tracking and analysis) - please do come back for the latest official release of Gravity Machine version 1.0 in a months time. Watch this space!