Deep learning modeling on the Project

Example of Model-building for Deep Learning

In this example, we used a mathematical model to define features in a library of microscopy movies, which allowed us to define features for extraction by a pre-trained model (DeepLabv3). 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.

Using digital data to understand biology

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.

Current state of the project

To see where we are in this project, please explore this repo, read our latest publications, or check out our collection of open datasets.

REFERENCES (numbered in alphabetical order):

[1] Sabater, S. (2009). Diatoms. Encyclopedia of Inland Waters, 149-156. doi:10.1016/B978-012370626-3.00135-6

[2] Jahn, R. and Schmid, A.M.M. (2007). Revision of the brackish-freshwater diatom genus Bacillaria Gmelin (Bacillariophyta) with the description of a new variety and two new species. European Journal of Phycology, 42(3), 295-312. doi:10.1080/09670260701428864.

[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.

[4] Gordon, R. (2016). Partial synchronization of the colonial diatom Bacillaria paradoxa. Research Ideas and Outcomes, 2, e7869.

[5] Poulsen, N.C., Spector, I., Spurck, T.P., Schultz, T.F., and Wetherbee, R (1999). Diatom gliding is the result of an actin-myosin motility system. Cell Motility and the Cytoskeleton, 44(1), 23-33.

[6] Kapinga, M.R.M. and Gordon, R. (1992). Cell Motility Rhythms in Bacillaria Paxillifer. Diatom Research, 7(2), 221-225.

Additional References

Dr. Thomas Harbich's Internet Resource for Diatoms