BIO 346: Introduction to Microscopy and Image Analysis



Drosophila larval hemisegment, 20x

      Spring 2004 

Capsella  ursa-pastoris, 25x

Fri @ 1:10pm, Higley 307
 Instructor: K.L. Edwards

Higley Room 214 

Office Hours  M,W 10-noon, T2:30-3:30

     PBX 5398




Text: Barbara Foster. 1997. Optimizing Light Microscopy for Biological and Clinical Laboratories.  ASCLS.  Kendell/Hunt Publishers.

This laboratory is a practical course (not an experimental course) in light microscopy.  It is designed to give you a theoretical basis in and a "taste" of the power and limitations of light microcopy as an investigative tool. 

Microscopy and image analysis protocols require time, diligence/patience, respect, and care.  Some protocols may require weeks of work prior to observation.  You must invoke patience and utilize great care to maximize the chances for successful outcomes.  People proceed at different rates and returning to lab during the week to complete exercises is encouraged, rather than racing through them and garnering less.

The pedagogy of the class is one of cooperative and collaborative learning.  Discussion/queries/advice shared amongst us in the class is highly encouraged.  I thank this and every class for informing changes that make this course a more effective and fruitful one.




1. Attendance


2. Inquisitive and helpful attitude, diligence and perseverance.


3. Respect and care of the equipment (its all very expensive)


4. Project reports, both oral and annotated PowerPoint, as requested. (library and lab work)


5.  2 laboratory exam/practical.




Your grade is based on the quality of your lab practicals (20% each) and quality of your oral reports displayed in annotated PowerPoint (35-40%); class discussion and interaction (10-15%); and on your attitude, initiative and problem solving in lab, your laboratory methodology, and fulfilling obligations to the rest of class (10-15%).  Missing a lab without permission or excuse from the Dean’s office will automatically drop your grade by 2/3 of a letter at the least.






   Human sperm, 1500x

Mouse tongue epithelia,  170x


 BIO3 46: Introduction to Microscopy and Image Analysis



TEXT:   Barbara Foster. 1997. Optimizing Light Microscopy for Biological and Clinical Laboratories.  ASCLS.  Kendell/Hunt Publishers.

This is the first offering of this specialized laboratory.  Due to facility and staff reasons, the course will be a “rough draft”, something in the making that we will shape together.

Thus the syllabus is not written in stone.  We may not complete all; we may go further.  We may head into other avenues of microscopic inquiry.  Students and the instructor will present materials on aspects of microscopy and analysis throughout the course.







¨Lab                      ¨Links

January  16

Early history of microscopy:  The single lens microscope

pp 141-142

Make single lens microscopes




The dissecting and compound/inverted microscopes: Parts, use, care (Olympus CH2 video).

Kohler alignment/illumination


Ch. 1


Observe organism’s cellular structure and its development with dissecting and compound microscopes.  Submit drawings and description of organism.




The nature of light and lenses


Student presentations on how the eye “sees”:

visualization, retina structure and thresholds, optic nerve and brain decoding, color and contrast sensitivity

Ch. 2

Ch. 8

Kohler handout

Quantification: determination of actual magnification and making cellular measurements (handout)

eronomics of microscopy viewing


light and lenses

oil immersion

   February  6    


Nature of light and lenses cont.

Optimizing contrast techniques

Chp 3

Chp 4


Handout on Airy disk

Diffraction and Airy disk

Airy disk

concepts and formulas



Optimizing contrast techniques


Ch. 5



Lab test

contrast techniques



oblique illumination


Phase contrast microscopy


 Ch. 6
 Ch. 5

Phase Contrast

Hoffman Modulation Contrast


Polarized light microscopy


Ch. 7:

pp. 78-88

Convert a compound brightfield microscope to polarizing.  Handout: polarized light and biological organization



Spring Break




Histology: the art of specimen preparation and slide making






Differential interference microscopy: DIC Histology cont. (sectioning with Spencer Microtome)

Ch. 7: pp.89-95

compares phase contrast and DIC images

April 3

Fluorescence microscopy and image capture

Ch. 7: pp. 72-78

Ch. 9


Digital imaging


Limitations to light?  Electron microscopy Histology cont.

Ch. 10: pp 137-140



Limitations to light microscopy? Viewing individual molecules in action with the light microscope.


Lab test


interferometry...interference microscopy innovation




Deconvolution and Confocal microscopy: 3D imaging

Ch. 10: pp. 133-134

Getting a stereo image from a compound microscope

Resolving and quantifying in 3D (if system software is working)



     May 1       

Student Presentations: Literature examples of how light microscopies are used to advance biological questions/research.





Click here to access the quiz sets for this course.
Click here to access online reading assignments.