Template:Virtual Cell Exercises

From Computational Cell Biology

Open Virtual Cell using directions provided.

Create a login name and password. This will last beyond the length of the workshop.

We will examine the FRAP Tutorial to introduce Virtual Cell architecture and commands.

===Relevance of FRAP to courses===Template:Hide

Needed: Image stack, image analysis data

To obtain Image stack: 1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ). 2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis: 1. Use image analysis software to extract pixel values for fluoresence intensity 2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

(See print out for equations)

To normalize data across images vs. (t/msqi)

Tasks: 1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation What is needed in the simulation for an accurate comparison to experiment?