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Lab 1b: Can you learn any biology from physical measurements?

Analysis of Cell Motion Using ImageJ.

In this one-week lab, students are introduced to digital image analysis. We utilize ImageJ, a freeware program widely used in biomedical research, to analyze short video clips of biological motion. We use the question “For a simple cut, should a doctor prescribe antibiotics?” to open a discussion of the biological context of this lab: the immunological response of a wound to bacterial infections. Students analyze videos of wound-closure, bacterial motion, and neutrophils (white blood cells) to determine their relative speeds. The surprising result (that bacteria are ~30X faster than neutrophils) prompts students to think about both the validity and the implications of their numerical results. The students re-examine their underlying assumptions about how neutrophils operate and hypothesize what mechanisms enable the human body to defend itself in the absence of antibiotics.

Files for Students:

• Lab 1b: Can you learn any biology from physical measurements? Analysis of cell motion using ImageJ
• Pre-readings: 
• Introduction to ImageJ (pdf) (web version)
• ImageJ quick reference sheet (pdf) (web version) 
• Technical introduction to ImageJ 

Files for TAs:

• Lab 1b: TA Guide

Media Files:

• Video files to analyze (smaller)
• WoundHealing
• Neutrophils
• E_Coli

• Video files to view (larger):
• WoundHealing.mp4
• Neutrophils.avi
• E_Coli.avi
• Once upon a time... Life - The blood (1 of 3) (hq)_31-60s.mp4-.mp4 (Great cartoon video showing the nuetrophils as 'police' who chase down and eat the bacteria)
• Neutrophil Extracellular Trap (hq)_0-12s.mp4-.mp4 (A fancy computer simulation showing the neutrophil chasing down and phagocytizing bacteria)
• Neutrophil Extracellular Trap (hq)_12-64s.mp4-.mp4 (Play this at the end of the lab time--this tells an interesting, newly-found capability of  neutrophils to use their DNA as a sticky trap, a NET, for bacteria.)

Pre-reading Response Prompt:

In one or two paragraphs, please describe what you found interesting in your exploration of ImageJ. (For example: Did you find an interesting image in the Cell Image Library? Did you discover a fascinating functionality of ImageJ? Did you find an application of ImageJ that sparked your interest? Why did you find this thing interesting?)

Kim Moore, Spring 2014