# 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)](https://github.com/devoworm/Digital-Bacillaria/blob/master/Tutorials/TensorFlow-using-DeepLab.md). 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.

[![](https://user-images.githubusercontent.com/19001437/60073556-66a14400-96e6-11e9-913d-188015b3f8f1.jpg)](https://user-images.githubusercontent.com/19001437/60073556-66a14400-96e6-11e9-913d-188015b3f8f1.jpg)<br>

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].

[![](https://user-images.githubusercontent.com/19001437/58767418-47345280-8550-11e9-987c-9e302567e55c.png)](https://user-images.githubusercontent.com/19001437/58767418-47345280-8550-11e9-987c-9e302567e55c.png)<br>

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](https://github.com/devoworm/Digital-Bacillaria/tree/master/Manuscripts), or check out our [collection of open datasets](https://github.com/devoworm/Digital-Bacillaria/tree/master/Public%20Data).

### REFERENCES (numbered in alphabetical order):

\[1] Sabater, S. (2009). [Diatoms](https://www.sciencedirect.com/science/article/pii/B9780123706263001356). *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](https://www.researchgate.net/publication/249026177_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*](https://riojournal.com/article/7869/). *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](https://www.ncbi.nlm.nih.gov/pubmed/10470016). *Cell Motility and the Cytoskeleton*, 44(1), 23-33.

\[6] Kapinga, M.R.M. and Gordon, R. (1992). [Cell Motility Rhythms in *Bacillaria Paxillifer*](https://www.tandfonline.com/doi/abs/10.1080/0269249X.1992.9705215). *Diatom Research*, 7(2), 221-225.

### Additional References

[![](https://user-images.githubusercontent.com/19001437/60072607-a1ee4380-96e3-11e9-9187-77a4c69d8f4a.png)](https://user-images.githubusercontent.com/19001437/60072607-a1ee4380-96e3-11e9-9187-77a4c69d8f4a.png)<br>

[Dr. Thomas Harbich's](https://diatoms.de/en/site-notice) Internet Resource for [Diatoms](https://diatoms.de/en/)
