Deep learning modeling on the Project
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In this example, we used a mathematical model to define features in a library of microscopy movies, which allowed us to define features for . From this, we were able to create digital models of Bacillaria cells for further analysis.
This mathematical model used five points on each cell to define a bounding box:
The two ends of the cell (1 and 2).
The midpoint of the line formed between 1 and 2 (3).
The edges of a cell (4 and 5) defined by drawing a line perpendicular to the axis defined by points 1, 2, and 3.
Figure 3. A diagram showing the five points on a sample cell. Click to enlarge.
To get more information about what is currently going on, check out the issues and subdirectories of this repository.
One of our goals is to use the data extracted from microscopy images to better understand biological processes such as the movement of a Bacillaria colony. One such example that has been conducted with coarse-grained phenotypic models is to model the hydrodynamics of filament movement through the water column [6].
Figure 4. Examples of Bacillaria filament moving through the water column (represented as a flow field). Click to enlarge.
[3] Ussing, A.P., R. Gordon, L. Ector, K. Buczko, A.G. Desnitskiy and S.L. Van Landingham (2005) The colonial diatom Bacillaria paradoxa: chaotic gliding motility, Lindenmeyer Model of colonial morphogenesis, and bibliography, with translation by O.F. Muller (1783). Diatom Monographs, 5, 1-139.
To see where we are in this project, please explore this repo, read our , or check out our .
[1] Sabater, S. (2009). . Encyclopedia of Inland Waters, 149-156. doi:10.1016/B978-012370626-3.00135-6
[2] Jahn, R. and Schmid, A.M.M. (2007). . European Journal of Phycology, 42(3), 295-312. doi:10.1080/09670260701428864.
[4] Gordon, R. (2016). . Research Ideas and Outcomes, 2, e7869.
[5] Poulsen, N.C., Spector, I., Spurck, T.P., Schultz, T.F., and Wetherbee, R (1999). . Cell Motility and the Cytoskeleton, 44(1), 23-33.
[6] Kapinga, M.R.M. and Gordon, R. (1992). . Diatom Research, 7(2), 221-225.
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