BMED 8813 IC2: Spatial and Temporal Scales in the Nervous System Spring 2009 – Profs. Shella Keilholz (SK) and Garrett Stanley (GS) Introduction M Jan 05 Course Introduction – GS and SK In class: Pass out syllabus, make clear the overall goals of the course, the logistics of Modules 1, 2, and 3, introduce ourselves, have members of class introduce themselves, discuss the previous IC course, discuss expectations (familiarity with Matlab, etc) Assignment: Read syllabus and check out course website MODULE 1 – Spatial and Temporal Scales of Early Vision W Jan 07 Introduction to Module 1 – GS In class: Module 1 - introduce the perspective of visual art as a sampling problem, illusions, break into small groups to discuss, example illusion presentation Form Groups: small groups for discussion, larger groups for presenting motion/time illusions, draw from a hat for the particular illusion you will present, look up resources and take best guess at what is causing phenomenon (note that some of these will be spatial, some temporal, and mostly a combination – the goal here is to simply get us thinking about these things). Assignment: Read Perspective paper from Conway & Livingstone (2007), individuals each visit Illusion website (http://www.michaelbach.de/ot/) and experience at least 5 of these phenomena and write 2 or 3 sentences about your observations of each to turn in during next class meeting, each group prepare presentation on illusion assigned for next class meeting Resources: Conway and Livingstone (2007), http://www.michaelbach.de/ot/, Dr. Angry/Mr. Smile movies, etc. Sampling Concepts M Jan 12 Spatial Sampling In class: Illusion presentations by groups, discussion of spatial sampling, aliasing, space/frequency transformation BMED 8813 IC2 – Course Syllabus – Spring 2009 Form Groups: keep groups from 01/07 Assignment: Groups work on a short (1 page) writeup of the illusion they presented for handing in during next class meeting, Read SchynsOliva1998 paper, Assignment 1 - do sampling exercises in groups Resources: http://www.michaelbach.de/ot/, Dr. Angry/Mr. Smile movies, etc., Castleman chapters, some basic Matlab scripts to lead in the right direction W Jan 14 Sampling Problems In class: Groups turn in writeup of illusion, work in groups on Assignment 1 during the class meeting, write pseudo-code, and plan the work, assign problem for presentation at next class meeting Form Groups: Keep the groups formed on 01/07 Assignment: Each group to finish Assignment 1 and prepare presentation of a single pre- determined assignment problem and written version of all problems to turn in as a group at next class meeting Resources: http://www.michaelbach.de/ot/, Dr. Angry/Mr. Smile movies, etc., Devalois Chapters on Spatial Frequency Channels and Linear Systems, Castleman Chapter Anatomy/Physiology of early visual pathway M Jan 19 Official School Holiday – MLK W Jan 21 Anatomy and physiology of early visual pathway In class: Each group presents their assigned problem from Assignment 1, turn in written version of Assignment 1, form new groups for reading and presenting the findings of the anatomical studies (each group will be assigned a specific paper or set of papers to present) and for Assignment 2, Review anatomy/physiology of early visual pathway, same groups also read over and briefly discuss Assignment 2 Form Groups: Form new groups for anatomy studies and Assignment 2 Assignment: Assignment 2 - Spatial Filtering, work on in new groups Resources: Rodieck Chapters, Williams & Collier (1983), Yellott (1983), Snyder et al. (1986), Dacey and Petersen (1992), Dacey Review, Lorenceau (2003), McMahon (2000), Sanderson (1971), Synder (1986), Swindale (1997), Zhaoping (2006) BMED 8813 IC2 – Course Syllabus – Spring 2009 Anatomical Predictions of Spatial Fidelity M Jan 26 Implications of Retinal Sampling In class: Groups present the anatomical findings, to turn in short (1 page) writeup of anatomic findings at next class meeting, break into new small groups for open discussion on the implications of the findings, ask whether known anatomy predicts spatial fidelity of early vision, propose explicit experiments to more rigorously test this, revisit the Dr. Angry/Mr. Smiles problem, based on the transition point make estimates of filtering characteristics they used, revisit the Mona Lisa and make predictions about distance observer should stand relative to the painting Form Groups: Keep the groups formed on 01/21 Assignment: Continue working on Assignment 2 in groups, prepare presentation of single pre-assigned problem and written solutions to all problems to hand in collectively during next class meeting Resources: Williams & Collier (1983), Yellott (1983), Snyder et al. (1986), Dacey and Petersen (1992), Dacey Review, Lorenceau (2003), McMahon (2000), Sanderson (1971), Synder (1986), Swindale (1997), Zhaoping (2006) Temporal Scales: Motion and Change, and Physiological Predictions W Jan 28 Time vs. Frequency Domain and Temporal Sampling In class: Groups turn in short (1 page) writeup of anatomic findings presented during last class meeting, each group presents their assigned problem from Assignment 2, turn in written solutions to Assignment 2, form new groups for Assignment 3, work on Assignment 3 in groups in class Form Groups: new groups for Assignment 3 Assignment: Assignment 3 - Temporal Sampling and Filtering, work on in new groups, each group to present assigned problem at next class meeting and turn in collective written solutions to all problems Resources: Oppenheim & Shafer chapters M Feb 2 Time Scales of Neural Activity in Early Sensory Pathways BMED 8813 IC2 – Course Syllabus – Spring 2009 In class: Each group presents their assigned problem from Assignment 3, turn in written solutions of Assignment 3, discussion of time scales of retina Form Groups: keep groups from 01/28 Assignment: each group prepare presentation on pre-assigned paper for next two class meetings on neurophysiological measurements of spatial and temporal properties in the early visual pathway Resources: papers on retinal time scales Measurements and Experiments W Feb 4 In class: group presentations on early visual neuron spatial tuning property papers, to turn in short (1 page) writeup of findings during next class meeting Form Groups: keep groups from 01/28 Assignment: Groups presenting today to turn in short (1 page) writeup of findings during next class meeting, remaining groups continue working on presentations for next meeting period Resources: Spatial Tuning Property Papers M Feb 9 In class: group presentations on early visual neuron temporal tuning property papers, to turn in short (1 page) writeup of findings during next class meeting Assignment: Groups presenting today to turn in short (1 page) writeup of findings during next class meeting Resources: Temporal Tuning Property Papers BMED 8813 IC2 – Course Syllabus – Spring 2009 MODULE 2 – Spatial and Temporal Scales of Imaging Modalities Functional Networks and Brain Imaging W Feb 11 In class: Discussion of modularity and network organization in the brain. Introduction to imaging, discussion of spatial and temporal scales for both imaging and neural activity. Assignment: Assignment 4: presentation and short report on an imaging modality Due: M Feb 16 In class: Group reports on functional imaging modalities. Assignment: finish report on imaging modalities. Due: Assignment 4 presentation Modeling the Measured Response to a Stimulus W Feb 18 In class: Build a conceptual model of how a stimulus-induced change in neural activity might affect the signal in a functional image. Assignment: Assignment 5: research one of the missing links in the model. Present and prepare a short report. Due: Assignment 4 report. M Feb 23 In class: Group presentations for assignment 5. Assignment: Read Logothetis review and finish assignment 5 report. Assignment 6: Pick an unknown and design an experiment to address it. Specific aims pages will be due Wednesday Mar 4. Due: Assignment 5 presentations. BMED 8813 IC2 – Course Syllabus – Spring 2009 Functional Studies of the Visual System W Feb 25 In class: Discussion of Logothetis review. Assignment: Assignment 7: presentation and short report on modularity paper. Due: Assignment 5 reports. M Mar 2 In class: Each group presents assignment 7 findings. Assignment: Finish assignment 7 reports. Revisit Assignment 6: propose an experiment to fill one of the missing links or to test a prediction of the model. A one page summary is due on Wednesday by email and will be sent out for study section review in preparation for Monday’s study section. Each group will be assigned a proposal to present. Due: Assignment 7 presentations. W Mar 4 In class: Practice study section using the 6 specific aims papers by GS and SK. Rank the proposals and fund 2. Assignment: Each group will act as primary reviewer for one proposal and present its merits and weaknesses on Monday. Due: presentation of mock aims, assignment 7 reports, assignment 6 summaries. M Mar 9 In class: Study section using class proposals. Write reviewer feedback. Assignment: Assignment 8. Revise experiments based on reviewer feedback. Produce final report, due Monday after the end of the module. Due: W Mar 11 In class: Discussion of data analysis and experimental interpretation. BMED 8813 IC2 – Course Syllabus – Spring 2009 Assignment: Due: MODULE 3 – Proposals and Critical Review M Mar 23 In class: Review and discussion of material presented in class to date; identification of gaps in the current literature. Assignment: Assignment 9: Identify a topic for proposal and be prepared to present it on Wednesday. Be succinct! Each person will have 2-3 minutes. Due: Experimental design and specific aims from module 2 W Mar 25 In class: Presentations on proposal topics. Assignment: Read experimental designs for review on Monday. Due: Assignment 9 presentation M Mar 30 In class: Review of experimental designs from module two, lead by instructors. Assignment: Assignment 10: Detailed outline of proposal, to be presented Wednesday. Due: Assignment 9 report (half page). W Apr 1 In class: Small group presentations for assignment 10. Each person should plan on discussing his or her proposal for 15-20 min. Assignment: Assignment 11: Prepare individual presentations of proposals (~15 min) Due: Assignment 10 presentations. BMED 8813 IC2 – Course Syllabus – Spring 2009 M Apr 6 through W Apr 15 In class: Presentation of individual proposals. Another student will provide a summary for each presenter, due the next day to the presenter and the instructors. Assignment: Assignment 12: review of individual proposals and Assignment 13: final reports Due: Assignment 10 outlines (3/6), assignment 11 presentations (ongoing), assignment 12 reports (ongoing). Assignment 13 is due Friday April 17. Week of April 20 In class: Long study section on final reports. Each student will be assigned two reports to review. Assignment: Assignment 14: reviews of final reports. Due: Assignment 14 is due first day of finals week. Summary of Assignments 9: Two minute presentation of final proposal topic and half page writeup. 10: Detailed outline of proposal and informal presentation. 11: Formal presentation of proposal. 12: Written review of (someone else’s) proposal presentation. 13: Final written proposals. 14. Written review of two other final proposals.
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