Fall 2002 


                                                                                                             photo from Molecular Probes


   4:00-6:00 pm
   Foster Hall 110

  Instructor: Dr. Elba E. Serrano
  Associate Professor of Biology
  Ph.D., Stanford University

  Office & Office Hours:

 Foster Hall 337D
 Wed 12:15-1:15 pm
 (&  by  appointment)
 Contact the Instructor:



Biology 550,  Principles of Confocal Microscopy covers the fundamental principles and applications of confocal microscopy.  The class format includes lectures, student presentations, and a lab practicum. Slides sets will be provided for the hands-on portion of the course.  Students will learn to operate the BioRad 1024 in the Fluorescence Imaging Facility.  Upon completion of the course, participants will have the tools to develop an experimental protocol for a confocal imaging study in an area of research interest and will have the foundation for more intensive studies of confocal and fluorescent imaging technology.  Students who successfully complete the course may petition to be independent users of the BioRad 1024 confocal microscope in the NMSU FIF.
* Cell Organismal graduate students receive Tier II credit for the course.
Recommended:  Molecular Cell Biology (Bio 520), Instrumental Methods (Chem 471),  and Optics (Physics 470).

Required Text
Recommended Text
Textbooks can be obtained at the bookstore or online from vendors such as Amazon and ecampus or Best Book Buys

Students committed to professional careers in microscopy are encouraged to purchase the Handbook by Pawley.

 no image available
Imaging Neurons (2000)
   Yuste, R., Lanni, F. and Konnerth, A
    Cold Spring Harbor Press 
    ISBN : 0-87969-541-2
Handbook of Biological 
Confocal Microscopy
 2nd edition (1996)
Pawley, J.B. 
Plenum Press, New York, New York
ISBN 0-306-44826-2

Lectures will highlight key concepts from the texts, journals, and web pages.   Students are responsible for mastering the concepts in the readings whether or not they are discussed in class by the instructor.  The instructor is available to discuss material from lectures and readings during scheduled office hours and by appointment. .

Sept 3 Introduction
Basics of Confocal Microscopy
Sample Preparation
BioRad 1024 System 
Sept 10 Safety Concerns & FIF User 
BioRad 1024 System Access
Confocal Optics 
Fluorescent Probes
  • Readings from  Imaging Neurons 
  • Appendix 3 Care and Cleaning of Optical Equipment
  • Appendix 4 Cautions
  • Ch 1  Microscopy and Microscope Optical  Systems
  • Chapter 11 Confocal Microscopy: Principles and Practice 
  • Chapter 12 Practical Limits to Resolution
  • Select topic for pesentation (use  list for ideas)
  • Access the following web sites and browse contents
  • Order Bio-Rad fluorophore poster
  • Order Molecular Probes Product CD and or book

    Sept 17 Practicum Preparation
    Student Presentations (3)
  • Practicum Week
  • Lasersharp Manual
  • Use fluorescent probe database
  • Flourescence basics review
  • Readings from  Imaging Neurons 
  • Appendix 1 Glossary
  • Appendix 3 Lenses, Filters, Spectra
  • Sept 24 Practicum Discussion
    Student Presentations (3)
  • Practicum Week
  • Oct 1 Practicum Discussion
    Fluorescence Energy Resonance 
       Transfer  (FRET )
    Student Presentations (3)
  • Practicum Week
  • Imaging
  • NIH Image
  • Imaging Programs (Keck - Univ of Washington)
  • Readings from  Imaging Neurons 
    • Ch 18 Lasers
    • Ch 55 FRET
    Oct 8 Practicum Discussion
    Image Processing: Metamorph, 
        Image J, etc
    Calcium and Proton Imaging
    Student Presentations (3)
  • Imaging
  • NIH Image
  • Imaging Programs (Keck - Univ of Washington)
  • Readings from  Imaging Neurons 
    • Ch 30 Calcium Indicators
    • Ch 31 Quantitative Calcium Fluorimetry

    • Ch 32 Calcium Indicator Calibration 
    Oct 15 Spinning Disk Scanners
    Multi-Photon Microscopy
  •  Readings from  Imaging Neurons 
  • Ch 17 Principles of MP Microscopy



      Earning Grade Points:  Grades will be calculated by adding the total points earned on all assignments and presentations.  A total of 500 pts may be earned during the course. YOU MUST TAKE THE FINAL EXAM.
      In class participation : (70 pts)  Based on your contribution to class discussion and evidence of preparedness for class. 

      Presentations: (70 pts)  Based on your contribution to class discussion, presentations, and evidence of preparedness for class.  Suggested topics:

    • PMT technology
    • tunable lasers
    • scanning disk confocal imaging
    • FRET
    • fluorophore colocalization 
    • vital imaging
    • fluorophore physical chemistry and synthesis
    • ion imaging
    • image reconstruction and processing
    • see texts for additional ideas
    • journal articles that address applications of confocal imaging to research topic of interest
    • Exams:  (100 pts) There will be one final exam during finals week.

      Term paper: (150 pts)   The term paper will consist of a proposal for a confocal study.   Topics should be selected in consultation with the instructor.   Details of what should be included in the term paper and how to organize the term paper  will be posted here: INSTRUCTIONS .  The term paper will be due Nov. 15, 2002

      Assignments (110 points) You will be required to complete assignments related to the lab practicum.   These assignments will be announced in class and  will be posted on this web site

      Grade Scale: The grade scale may be curved at the end of the semester at the discretion of the instructor.
        A     450-500 pts
        B     400-449 pts
        C     350-399 pts
        D     300-349 pts
        F     < 300 pts
        S     (Satisfactory) requires a C-
        S/U Option: Students must meet all requirements of the course.  A grade of C- is required  to receive an S in the course.
      Attendance Students are responsible for all material covered in class as well as any previously unannounced assignments that are given out in class.  Therefore  students are expected to attend all classes.  Contact the instructor BEFOREHAND if you will be unable to attend class.



    Late assignments. 10% of the total points will be deducted for each week the assignment is late. Assignments will not be accepted if handed in more than 2 weeks after the due date

    Syllabus Modification: The instructor reserves the right to modify this syllabus during the semester as considered necessary to enhance the quality of the instruction, to meet the needs of students in the class and to achieve course objectives. Any changes to the syllabus (or to the course schedule) will be announced in class and you are responsible for being aware of them.

    Students with Disabilities:

    • If you have, or believe you have, a disability and would benefit from any accommodation(s), you may wish to self-identify by contacting the Services for Students with Disabilities (SSD) Office located at Garcia Annex [phone 646-6840; TTY 646-1918] to register.
    • If you have already registered, please make sure that your instructor receives a copy of the accommodation memorandum from SSD within the first two weeks of classes.
    • It will be your responsibility to inform either your instructor or SSD representative (in a timely manner) if the services or accommodations provided are not meeting your needs.
    • If you have a condition that may affect your ability to exit safely from the premises in an emergency or that may cause an emergency during class, you are encouraged to discuss any concerns with the instructor or with the SSD Coordinator.
    • Feel free to call Ms. Elva Telles, EEO/ADA & Employee Relations Director, at 646-3333 with any questions about the Americans with Disabilities Act (ADA), and/or Section 504 of the Rehabilitation Act of 1973.  All medical information will be treated confidentially.
    Code of conduct::   Please see the Student code of conduct in the current Student Handbook.  Pay particular attention to the sections on Academic Misconduct and Plagiarism. The penalty for plagiarism or other forms of academic misconduct (as defined in the Student Code of Conduct) is failure of the course: no exceptions.


    GUIDELINES FOR CLASS DISCUSSION:  During the semester, different  opinions may be voiced in the class. You may strongly disagree with some of these, or you may find them amusing. Outbursts can be misinterpreted and are counterproductive to meaningful and thoughtful debate. Therefore, it is important that you exercise self-discipline and self-control, and treat all members of the class with the courtesy  you are entitled to receive in turn. The key words are respect and courtesy. Thank you!

    XEROX and/or BACKUP all assignments before submitting them to the instructor.

    SAVE xeroxes of all graded assignments and exams from this course at least until you have received your final grade.

    WITHDRAWALS:  It is your responsibility to withdraw from the course.
    DEPARTMENT OFFICE:     The Biology Department office is in FOSTER HALL 234, 646-3611.  The department secretaries are Ms. Gloria Valencia and Ms. Reta Akers.

    DEPARTMENT CHAIR:     The Biology Department chair is Dr. Laura Huenneke.  Her office is in FOSTER HALL 234 (X63611).

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