Senior Design Projects

ECS193 A/B Winter & Spring 2021

Interactive 2D Fourier maps of cells

Email **********
Name Gerald Quon
Affiliation UC Davis (Department of Molecular and Cellular Biology)

Project's details

Project title Interactive 2D Fourier maps of cells
Background The Fourier and 2D Fourier transforms are well-studied transformations that have a wide range of applications in signal processing. When applied to images, Fourier transforms can be used in applications such as denoising.

Recently, molecular biologists have started to produce large 2D maps of slices of human tissue. The data these biologists produce can be viewed as a 2D grid, where each ‘pixel’ in the grid takes on a one-of-K encoding (corresponding to identification of one of K types of cells, or ‘no cell’). Figure 1 illustrates an example of this data.
The goal of biologists is now to look at these 2D images of cells from tissues like the brain, and identify ‘spatial motifs’, or recurring patterns of groups of cells (see Figure 2).
Description Students working on this project will implement a GUI that performs the following tasks:
(1) Load a biological image;
(2) Visualize the raw biological image (e.g. Figure 1)
(3) Visualize the 2D Fourier transformation of that image
(4) Provides interactive controls to allow filtering of the Fourier coefficients of the image
(5) Provide a reconstruction of the image (after filtering is applied)
Deliverable (1) A working prototype of the GUI, implemented either as a standalone package, or with a web interface.
(2) Code that implemented the app submitted to a GitHub repository.
(3) Comprehensive documentation of code.
Skill set desirable Python programming
Phone number **********
Client time availability 30-60 min weekly or more
IP requirement Open source project
Attachment Click here
Selected No
Team members N/A