1. Graphical User Interface on Analysis of Mechanics and Dynamics of Biopolymers in Living Cells Peter Russel, Biomedical Engineering Shubham Agrawal, Computer Engineering Abdel-Rahman Hassan, Biomedical Engineering Professor Taeyoon Kim, Biomedical Engineering

2. Introduction Cell mechanics, the physical response of cells to stimuli, depends in part on the qualities of the cell’s filamentous actin (f-actin, for short) such as elongation. These quantities characterize the f-actin and if changed can indicate if a stimulus added to the sample is affecting the cells cytoskeleton, and by extension mechanical properties. The ability to quickly analyze microscope images of their cell samples will be of great use to cell biologists investigating the behavior of these filaments.

3. Motivation for the entire project As of yet there exists no software able to quickly and efficiently track and analyze filamentous actin filaments from a live cell image Given the number of filaments in an image, and the number of images in a sample, manual tracking is impractical. For example, here is a microscopic image of filamentous actin: This project is to create such a software

4. Motivation of the Graphical User Interface Original Image (in vivo) Tracked Filament

5. The Graphical User Interface The main screen:

6. Input & Output The Input is a ‘.tif’ image, Output is a text file The User browses for image file input and can either browse, or create a new file, from the text line

7. Variables ‘Sensitivity’ Controls the expected contrast between filament and background Higher contrast factor limits the track more ‘ μ m/pixel’ is how long one pixel width is in micrometers

8. Sensitivity Factor Effect Sensitivity factor of 0.1Sensitivity factor of 0.3

9. ‘Go!’ Function – Filament Selection 1) User prompted to select filaments to track

10. ‘Go!’ Function – Filament Tracking 2) The Program tracks a filament from the first selected point, presents the track, and gives the user three options: Accept, Delete and Modify

11. Modify Button Press & Functionality Modify interface appears: Allows user two options Trim the result Retrack with a new sensitivity The user accepts or deletes the filament from the Modify GUI, can cancel at any time. The user can also continue to modify the result indefinitely

12. Trim Option As name suggests, allows user to shorten the track result manually when the user believes the filament tracking has tracked too far.

13. Rest of Program & Output Goes through each point selected initially in the same manner, tracking and allowing for modification. Each filament’s contour length is calculated after tracking is finalized with all contour lengths being compiled for entire image. This is returned as the output along with a data file:

14. Conclusions This program will allow users to analyze more of their data at less time, thereby helping cytoskeletal filament researchers characterize their samples with quantities such as elongation Additional work includes: Increasing the accuracy of the filament tracking software Allowing the program to track over many frames, thereby determining dynamic properties such as elongation rate Eliminating the need for users to select inputs

15. End of Presentation

16. Persistence Length Calculation

17. Program ‘Length Calculation’ Statistics Two sample T-test used to determine if the programs calculation of contour length was accurate. The first group is the FTracker calculated contour lengths of ten filaments. The Second group is ten filaments tracked using JFilament, an addition to ImageJ, in this the tracks are drawn by hand and is taken to be the ‘correct’ contour length. T value of 0.21 Critical value of 2.101 T < Critical; FTracker is statistically similar to JFilament