Graduate Course Descriptions

G100 Level Courses

Ocular Anatomy, Biochemistry & Physiology I
Semester Credits: 2.25

The Ocular Anatomy, Biochemistry and Physiology course covers the anatomy, physiology and biochemistry of the globe, related visual structures and the 
visual pathway.  Part I begins with an anatomical overview of the eye and related structures, providing the student with an introduction to the basic structural features of the eye. This is followed by the anatomy of the fibrous tunic and the 
physiological basis for corneal transparency and how the cornea regulates its hydration and metabolism. Uveal anatomy and the physiology of the ocular fluids follow.  The production of aqueous humor and its outflow through conventional and uveoscleral pathways leads to a discussion of intraocular pressure and its regulation. The neuroanatomical basis for papillary and accommodative responses and their clinical context follows. Finally, the 
anatomy, development, molecular composition and metabolism of the lens lead to a discussion of changes in the lens that occur during aging, including the biochemistry of cataract formation.

Ocular Anatomy, Biochemistry & Physiology II
Semester Credits: 3.25

OABP II is a continuation of OABP I.  It begins with the study of the anatomy of The vitreous, retina, optic nerve and visual pathway.  The biochemistry of the visual process including the biochemistry and molecular biology of rhodopsin and cone pigments and the events that occur during the visual cascade will be studied including a discussion of color blindness, congenital night blindness and hereditary retinal degeneration.  Nutritional and biochemical implications in age-related ocular disease will then be explored.  Processing of visual information by the retina, lateral geniculate nucleus and function of the ocular appendages and the physiology and biochemistry of the tear film.  The course ends with the study of the development of the eye and visual system. Integration with material taught in Gross Human Anatomy and Neuroanatomy is integral to the understanding of 
the structure and function of the eye and is emphasized in the course.

G200 Level Courses

Introduction to Statistics
Semester Credits: 2

This course is intended as a broad overview of basic statistical principles and methods for the beginning graduate student.  Among the topic areas covered are: large and small sample hypothesis testing; experimental design, analysis of variance; parametric and non-parametric tests and correlations.

Prerequisites: Undergraduate statistics or permission of instructor.

Optics of the Eye
Semester Credits: 2

This seminar examines the role of natural “aberrations” from the environment (optical vergence) and from refraction and chromatic dispersion across the extended pupil of the chambered vertebrate eye, especially the role of defocus and chromatic aberration.  We consider the hypothesis that defocus and chromatic aberration specify optical vergence, distance and relative depth, monocularly and binocularly, as polychromatic blur across the retina in conjunction with polychromatic apodization across the exit pupil of the eye and that modulation/phase across both retina and pupil are potential signals for accommodation, emmetropization and visual perception.  Readings explore the nature of the retinal image, blur from diffraction, defocus and aberrations, the Stiles-Crawford effect, sensitivity of the visual system to wavefront spherical curvature (optical vergence) and chromostereopsis.

Prerequisites: Integrated Optics I and Proseminar: Introduction to Vision Science or the equivalent. Permission of instructor.

Spatio-temporal Processes: Basic Science & Clinical Applications

This seminar will cover basic and clinical topics on visual sensitivity and resolution, linear analysis, contrast sensitivity, retinal processing and hyperacuity.  Relevant clinical applications will be emphasized. Both classic and contemporary research literature will serve as the reading material for the course.

Prerequisites: Permission of instructor.

Color Vision:  Color Perception
Semester Credits: 2

This tutorial will build from fundamentals of aperture color matching to the most recent work on color appearance in material perception. The goal of the course is to make students think in depth about all aspects of color perception. There will be an emphasis on the way ideas have developed about these topics, to give a context to present foci of interest. Each tutorial will be focus on a specific topic and will be shaped by the background and interest of the student(s).  A partial list of topics to be covered include: 1) Color matching and the dimensionality problem 2) Color adaptation to simple and complex fields 3) Color induction from Mach bands to 3-D figural effects 4) Perception of illuminants and filters 5) Color and perception of material qualities.

Prerequisitie: Ph.D students only or permission of Instructor.

Color Vision: Basic Science and Clinical Applications
Semester Credits: 2

Topics included in this seminar are color matching, discrimination, specification and appearance; physiological processing of wavelength dependent information; and tests of color vision and related clinical applications. Discussions will center on both classic and contemporary papers.

Prerequisites: Permission of instructor.

Vegetative Physiology of the Eye
Semester Credits: 2

This seminar will concentrate on topics dealing with important ultrastructural, cellular and physiological events in the anterior segment of the eye. Specifically the students will be reading and discussing papers relating to lacrimal and corneal physiology and aqueous humor dynamics.

LGN and Cortex: Early Visual Processing of the Brain

Prerequisites: Permission of instructor
Semester Credits: 2

This tutorial will provide basic information on the role of thalamus and striate cortex visual processing. It will require reading classical and recent papers on topics related with thalammocortical processing. It will cover anatomy, physiology and computational models of sensory processing in the early visual pathway.    

Prerequisites: There is no specific prerequisite other than a genuine interest in the topics to be discussed and a willingness to read a large number of papers and write reports on the reading material. Open to PhD students only or permission of instructor. 

Ocular Motility
Semester Credits: 2

Description: Students in this seminar will review both classic and contemporary literature on oculomotor behavior, models and neurophysiology. This will include readings on saccadic, smooth pursuit and vergence eye moments, as well as vestibular and optokinetic nystagmus. This seminar should provide the student with a basic appreciation of issues, experimental procedures and findings in oculomotor science.

Prerequisite: Permission of instructor

Integrated Optics 

Semester Credits: 4.5

This introductory course, which integrates elements of geometrical, physical and visual optics will prepare the student for the challenges for clinical practice, as
well as the requirements of the National Boards. The lectures, in conjunction with the laboratories, will help the student develop and appreciation of the eye as an optical instrument, a practical understanding of the broad-based clinical applications of lenses, prisms and mirrors, and the basic consideration of lens design principles as applied to the eye and ophthalmic instruments. It will serve as a foundational information base and provide background knowledge for the higher level clinical and optometric courses and literature review. The instructional sequence is: Introduction to light, optics of thin spherical and astigmatic lenses, optics of spherical refracting interfaces, optics of mirrors,
optics of thick and thin prisms, fiber optics, Gaussian systems, Newtonian optics, system stops and field of view, introduction to Visual Optics and model eyes, axes and angles of the eye and Purkinje-Sanson images.

Visual Function: Sensory
Semester Credits: 4.5

This course covers monocular sensory processes and visual perception.  Topics 
include spatial and temporal visual processes; visual adaptation, color vision; 
psychophysical methodology; information processing; gross electrical potentials; 
basic visual action; and basic visual-cognitive processes. Topics are discussed in 
terms of their normal function and clinically relevant deviations from normal. The anatomical and neurophysiological bases for visual performance are 
examined and related to clinical testing. Laboratories emphasize the 
measurement of these functions in assessing the visual capacities of individual patients and the demonstration of relevant visual phenomena.

GM200 Level Courses

Binocular Vision – Three-D Shape Perception

Semester Credits: 2

This tutorial will address the fundamentals of 3-D shape perception.  It will require reading classical and recent papers on relevant topics an learning rudiments of projective and differential geometry and spatial statistics. The goal of the course is to make students think in depth about all aspects of 3-D shape. There will be an emphasis on the way mathematical ideas inform the study of shape perception.  A partial list of topics to be covered include: 1) Geometry of solid shape 2) Statistical shape descriptors 3) Perspective 4) 3-D Shape from pattern, shading, reflection, motion and disparity cures 5) Cortical processes of shape decoding 6) Shape illusions and symmetry.

Prerequisite: PhD only or permission of instructor.

Binocular Vision – Motor and Perceptual  Aspects of Vergence Eye Movements
Semester Credits: 2

This course is devoted primarily to the motor components of binocular vision, namely tonic, accommodative, disparity and proximal vergence. While sensory and perceptual aspects are considered, the emphasis is on static and dynamic aspects of the motor response, including bioengineering models and computer simulation.  

Prerequisite: Permission of instructor

Visual Perception: Depth Perception and Cue Combination 

Semester Credits: 2


This tutorial covers cues to depth and spatial layout and how they are combined by the visual system. Special emphasis is placed on binocular disparity.
 Students are strongly encouraged to work examples in Matlab to improve their
Understanding of Bayesian theory and theory of signal detection.

Prerequisite: Permission of Instructor. 

Visual Perception: Perceptual Learning 

Semester Credits: 2


This tutorial covers known forms of perceptual learning: learning to discriminate (differentiation), recalibration (including contingent recalibrations), cue 
reweighting and cue recruitment. Students are strongly encouraged to work
examples in Matlab to improve their understanding of Bayesian theory and theory of signal detection.

Prerequisites: PhD students only or permission of instructor.

Visual Perception: Current Research on Clinical Conditions Affecting Visual Space Perception 

Semester Credits: 2


Many clinical conditions impair patients’ abilities to visually perceive the spatial layout of their environment and to safely carry out visually-guided spatial-motor activities. Research into such impairments and their remediation has been increasing in recent years, in part due to increasing technical capabilities to conduct such research. In addition to producing a better understanding of these impairments and their potential for remediation, such research can also lead to a better understanding of the basic processes underlying perception and action in complex spatial environments. This seminar aims at a close reading and critical examination of some recent research in this area.

Prerequisites: Permission of instructor

Ocular Biochemistry : Biochemical and Nutritional Implications in Ocular 
Health and Disease

Semester Credits: 2 


Topics include general nutritional considerations, age-related macular degeneration, senile cataract, relationship to chronic systemic disease (cardiovascular disease, hypertension, diabetes)

Prerequisites: The professional course Ocular Anatomy, Biochemistry & Physiology I & II. Permission of instructor

Ocular Pharmacology

Semester Credits: 2 


Description: TBA

Prerequisites: Permission of Instructor

Ocular Pathology

Semester Credits: 2


This seminar will introduce the students to the pathophysiology of diabetic retinopathy, the glaucomas and macular degeneration. The seminar will explore the underlying molecular, cellular and biochemical processes that cuase the clinical findings that characterize these diseases. The objective is to have a better understanding of the pathogenesis of these blinding eye conditions.

Prerequisites: Permission of instructor


Semester Credits: 2


This course provides a comprehensive survey of the human accommodative system.  Topcis include: introduction/overview of accommodation, anatomy and physiology of the accommodation, pharmacology and neurology of accommodation, the component inputs to accommodation (blur, vergence, proximity, and tonic), static and dynamic aspects of accommodation, bioengineering models of accommodation, theories of presbyopia, and dysfunctions of accommodation and their remediation.  

Prerequisites: Permission of Instructor.

Pre-dissertation Research

Credits: 1 credit per 2 hours of research per week

Hours: Variable.
Prerequisites: Must have signed consent of instructor.

Visual Physiology of the Eye

Semester Credits: 2

This tutorial will assess the role of retinal mechanism in vision. The goal of the course is to make students think in depth about visual processing before the cortex. Each tutorial will focus on a specific topic; it is assumed that a basic familiarity with retinal and anatomy is present.  A partial list of topics to be covered include: 1) The very front end – current issues in receptor function 2) Visual adaptation from receptors to ganglion cells – how and where does adaptation take place 3) Is the Gaussian model of receptive field structure valid? 4) How parallel are parallel pathways in the retina 5) Temporal processing – can we take the retina for granted 6) Spatial processing – how have ideas developed since DeValois 7) Color in the retina and optimal modes of information processing 8) Single units and sensation – what are the criteria for linking physiology and psychophysics 9) Contrast gain control in the retina  10) From cones to ganglion cells; how specific is retinal wiring? 11) Spike trains of ganglion cells – what can we infer from them? 12) Across the visual field – how successful has the concept of magnification factor been in explaining eccentricity related changes 13) From retina to LGN – the development of ideas.

Prerequisites: Full-time students only or permission of instructor.

Visual Development

Semester Credits: 2

One or more of the following topics will be explored throughout the term (students decide which topics they would like to research:

  • Development of Visual Acuity

  • Development of  Contrast Sensitivity Function

  • Development of Binocular Sensory Function

  • Development of Ocular Motility

  • Development of Accommodation

  • Development of  Visual Fields

  • Development of  Refractive Error and Emmetropization

  • Development of  Color Vision

  • Development of Accommodative/Vergence Interactions 

Prerequisites: Permission of instructor. Students should have taken the professional 
course Children’s Vision and Learning.

Ethics in Research

Semester Credits: 1


This is a seminar for Graduate students examining the  Responsible Conduct of Research. Upon completion of this course, Students will demonstrate:  1)A heightened sensitivity to the code of ethical conduct required in biomedical research.  2) Understanding all of the IRB review process, including federal and local requirements involved in the conduct of human subject research, and in particular the 'consent process.' 3)Understanding all aspects of the IACUC process, including federal and local requirements for laboratory animal care and use. 4) Familiarity with the skills needed to identify critical aspects of human and animal ethical dilemmas and resolve them in a rationale and responsible manner. These will consist primarily of case studies and presentations 5)Misconduct in Science, including the role of graduate students, faculty, authorship, and misrepresentation of scientific data.

Prerequisites: None

Receptors and Cell Signaling Pathways

Semester Credits: 2


It is becoming increasingly evident that many of the systemic and ocular diseases requiring therapy are a consequence of inappropriate receptor regulation of a physiological response. Therefore many drugs are being targeted to correct some dysfunction in receptor or effector control of a response.  There are many examples showing that systemic and ocular diseases requiring therapy are a consequence of inappropriate receptor regulation of a physiological response. Accordingly, it is essential that students learn in more detail how receptors mediate responses so that they can make better decisions on their own about the intelligent use of a drug in future endeavors.  This course will expand on the background information which they obtained in introductory general and ocular pharmacology courses.

Prerequisites: Permission of instructor

Introduction to Vision Science:  Part I

Credits: 6


This course is Part 1 of a year-long course designed to give a basic introduction to the eye. The emphasis will be to provide a background to the physiology, biophysics and neurobiology of the eye. Lecturers will impart basis information and ideas and also stress current foci of research interest.  There will also be an emphasis on introducing research methods and their pitfalls.  Part I includes the following topic areas: 1) Image forming mechanisms of the eye: image formation in the eye: optics, pupil, accommodation, etc; control of growth and transparency of lens and cornea, physiology and biochemistry of the eye. 2) Retinal mechanisms for acquisition and transmission of visual information: retinal structure and contrast gain control, synapses and signals between neurons, color vision: genetics and physiology (including anomalous color vision); spatial-temporal mechanisms.

Prerequisites: PhD students only.

Introduction to Vision Science: Part II

Credits: 6


This course is Part II of a year-long course designed to give a basic introduction to the eye. The emphasis will be to provide a background to the physiology, biophysics and neurobiology of the eye.  Lecturers will impart basis information and ideas and also stress current foci of research interest. There will also be an emphasis on introducing research methods and their pitfalls. It includes the following topic areas: 1) Cortical mechanisms for extraction and interpretation of visual information: structure and function in LGN and striate cortex, binocular vision, shape and motion perception, space and scene perception, control and consequences of eye-movements, perceptual learning, extra-striate cortex and perception and attention and the control of neural processing.

Prerequisites: PhD students only.

GM300 Level Courses

Independent Study

Credits: 1 credit per 2 hours of independent study per week.

Hours: Variable
Prerequisites: Must have signed consent of instructor.

Human Refractive Error Development

Semester Credits: 3


The objective of this course is to discuss and evaluate theories for the etiology of refractive error in humans. Particular emphasis will be placed on the development of myopia and how this may be related to hereditary and environmental factors.

Prerequisites: Permission of instructor.

Accommodation Laboratory

Semester Credits: 2


The student will gain "hands-on" experience with a variety of instruments commonly used to measure static and dynamic accommodation in basic and clinical research. The lectures will involve discussion of the basic principles of operation (optics, electronics and mechanics) as well as the test protocol.  The laboratory component will involve use of some of the devices by the students, including the confirmation of selected and accepted important results from previous studies, as well as development and implementation of a closely supervised, restricted original research project to provide a true sense of accomplishment.

Prerequisites: Permission of instructor.

Stiles-Crawford Effect

Semester Credits: 2


This advanced seminar will address the fiber-optic or waveguide nature of retinal cones (and rods) and the consequences of the Stiles-Crawford effect for visual function (e.g. depth of focus, aberrations, amblyopia, etc). Methods of measuring the Stiles-Crawford function, formation of interfererence or modal patterns by retinal receptors, the issue of receptor disarray, and the effect of receptor orientation on visual location will be discussed. Finally the interaction between the Stiles-Crawford effect and the effects of ocular aberrations will be introduced.

Prerequisites: Permission of instructor.


Semester Credits: 2


This seminar provides an overview of the sensory motor and perceptual aspects of vision and amblyopia. In addition, recent neurophysiological advances in imaging of the amblyopic brain will be considered along with possible clinical therapeutic implications.

Prerequisite: Permission of instructor.

Structure, Function and Clinical Role of the Tear Film in Protecting the Ocular Surfaces 

Semester Credits 2


It is the intent of this course to provide an overview of the nature and structure of the tear film and its roles in modulating the ocular surface homeostasis.

Prerequisite: Permission of instructor.

G400 Level Courses

Dissertation Research

Semester Credits: 1 credit per 2 hours of research per week

Hours: Variable
Prerequisites: Must have signed consent of instructor.

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