BasicsCoursePhDprog-PeterEvennetApril2013

PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course April 2013

Setup -Fri 05 April

Setup of all needed course material in Small Auditorium

Equipment needed

• Microscopes
• Optical bench
• Spinning disk gadget
• Polarazing sheets
• Diffraction Grids
• Fluorescent samples
• Fluorescent Beads (Prepare slides)
• First day Handout for students
• Light torches
• cameras and monitors
• Cleaning stations for each table
• condenser screwdrivers for each microsocpe
• oil/DIC objectives for each microscope (next to stand)
• 2 polarization filters for each microscope

DAY ONE (8th April)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	09:30	FINAL PREP	Test everything works	LMF
9:40	10:25	INTRODUCTION	COURSE INTRO WHO is WHO? Round table	LMF TEAM	White board and pen
10:25	11:05	Session 1 Theory	PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles ( incl. Refraction-basics)	PETER EVENNETT (JAN)	Jan shortly showing airy pattern from hole in mirror at one of the teaching microsopes (+ screen)
11:05	11:15	BREAK	BREAK
11:15	11:50	SESSION 1 Practice SHORT (5min !!!) Rotation	capillary/plastic (Huisken) in oil demo Coin-in-cup demo red and green laser through milky water with black background	(PETE)Jan PETER BRITTA (SILKE)	*capillaries, oil * coin-in-cup, water *laser pointer, glass with "milky" water and black background
11:50	12:45	SESSION 1 Theory	Introduction to lenses (Lens demo fun) Lens aberrations (see colour fringes of lighting image with simple lens) Resolution, Numerical aperture Magnification	PETER EVENNETT	little lenses
12:45	13:45	LUNCH	LUNCH
13:45	14:45	SESSION 1 Practice 15min (!!!) Rotation (Davide will watch the time)	Milky Glass Block demo Show and discuss microscope parts (upright and inverted) NA measurements	JAN BRITTA SILKE	*milky glass block, teaching microscope, coloured filters for microscope, iris objective *slides with arrows, simple upright and inverted microscope *horizontal protractor on stand, objective holder, 2 air objective with different (!) NAs (and maybe an iris objective), calculator, pencils, rubber
14:45	15:30	SESSION 2 Theory	Microscope illumination Conjugate planes	PETER EVENNETT
15:30	15:45	BREAK	BREAK
15:50	17:05	SESSION 2 Practice (30min Rotation)	conjugate planes on Peters microscope conjugate planes on optical bench	PETER EVENNETT JAN	*Peters microscope setup *optical bench demonstrating a transmitted light microscope, incl. light source
17:05	17:25	SESSION 3 Theory	Koehler Illumination Epi illumination (Microscope alignment)	PETER EVENNETT
17:15	18:30	SESSION 3 Practice	Koehler illumination (Microscope alignment)	LMF TEAM	students manual microscopes, screwdrivers, nice brightfield sample

DAY TWO (9th April)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:00	Recap	day 1	LMF TEAM	Questions
10:00	10:45	SESSION 1 Theory & Practice	Eyepieces Depth of Field Depth of Focus	PETER EVENNETT LMF TEAM	students microscopes with 10x/0.25 and 40x/0.65 objectives Stereoscope with a "sample"
10:45	11:00	BREAK	COFFEE BREAK
11:00	11:30	Session 2a DEMONSTRATION	Diffraction and Diffraction slide fun Diffraction string show	PETER EVENNETT	Diffraction slides, torch, "dashed" string
11:30	12:45	Special: MPI Technology Day (large auditorium)	talks from GE Healthcare Nikon Zeiss	Dan White Niklas Senghaas Olaf Selchow
12:45	13:30	BREAK	LUNCH
13:30	14:30	SESSION 2b Demo and Theory	Peter's Diffraction setup LIVE or Dan's diffraction setup demonstration	PETER or SILKE	Dan's ABBE Diffraction demo setup
14:30	15:15	SESSION 3 Theory and Demo	Lens aberrations and corrections	PETER EVENNETT JAN	magnetic lens + laser suitcase on white board|
15:15	15:45	SESSION 4 Theory	Introduction to contrast	PETER EVENNETT
15:45	16:00	BREAK	COFFEE BREAK
16:00	16:20	SESSION 4a Theory	Dark Field microscopy	PETER EVENNETT
16:20	16:45	SESSION 4a Practice	Dark Field microscopy	LMF TEAM	diatome slides
16:45	17:05	SESSION 4b Theory	Basics of Phase Contrast microscopy	PETER EVENNETT
17:05	17:45	SESSION 4b Practice	Phase Contrast microscopy	LMF TEAM	cheek cell samples

DAY THREE (10th April)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:00	Recap	day 2	LMF TEAM	Questions
10:00	10:30	SESSION 1 Theory	Objective reading	PETER EVENNETT LMF TEAM	objectives, eyepieces, polylux
10:30	10:45	BREAK	BREAK	BREAK
10:45	11:45	SESSION 1 Practice Group rotation	Cover glasses, sample mounting and Objective cleaning Objective reading	JAN BRITTA, SILKE	Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter at least 7 different, "interesting" objectives (for a group of 6-7)
12:15	12:45	SESSION 2 Theory	Polarized light microscopy	PETER EVENNETT
12:45	13:45	BREAK	LUNCH
14:00	14:40	SESSION 2 Practice	Polarized light microscopy	LMF TEAM	Hair, stone samples, benzocain cristals, rulers, gummi bears, plastic dishes, ...
14:40	15:05	SESSION 3 Theory	Differential Interference Contrast (DIC)	PETER EVENNETT
15:05	15:40	SESSION 3 Practice	Differential Interference Contrast (DIC)	LMF TEAM	cheek cell samples
15:40	16:00	BREAK	BREAK	BREAK
16:00	16:15	Question round	Questions to Peter Evennett	PETER EVENNETT LMF TEAM
16:15	17:50	SESSION 3 Theory & Practice	Detectors	BRITTA	• CCD chip • example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope

DAY FOUR (11th April)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	DEMO Activities	Materials needed
9:00	10:00	Recap (Demo)	day 3	LMF TEAM (JAN)	PIXELS	Sesame seeds, sunflower seeds, nudels, gumibears and a checker board (on Polylux)
10:00	10:45	SESSION 1 Theory	Fundamental concepts of fluorescence	JAN	-	fluorescent liquids in bottles plus laser pointer (blue, green, red)
10:45	11:00	BREAK	BREAK	BREAK	BREAK	BREAK
11:00	12:15	SESSION 2 Theory & Practice	Fluorescence Microscopy	DAVIDE	• Light sources • Lamp houses • Spectra • Filters • Filter cubes • Filter spectral charts of each microscope (laminated)	• Spare lamp houses • Lamps • Ocean optics equipment • Four (4) different Filter-sets (cubes), with the appropriate descriptions • diagramms for drawing filter/fluorophore spectra
12:15	13:00	SESSION 2 Practice	Fluorescence imaging at microscopes	LMF TEAM	-	• Fluorescent labeled samples (Convallaria)
13:00	14:00	BREAK	LUNCH	LUNCH	LUNCH	LUNCH
14:00	15:45	SESSION 3 Theory & Practice	What is a pixel Analog to Digital conversion Nuyquist-Shannon Quantitative Imaging Spatial Calibration	BERT DAVIDE	-	• pixel size calculation on a given optical setup
15:45	16:00	BREAK	BREAK
16:00	18:00	SESSION 4 Practice	Imaging with CCD cameras using LMF systems	LMF TEAM	• Displaying • Pixel size • Look up table • Binning • Exposure time • Saturation • Signal to noise • ROI • Bit depth • Auto map • Auto contrast	• Microscopes: DVcore(Davide, 3 students) N-Storm (Britta, 3 students) W1 Oly-TIRF (Bert, 3students) self-built-syst (Jan, 3 students)) • Fluorescence Sample slides (Kidney / Cells) • camera example sheets
19:00	open end	Dinner	with Peter	LMF TEAM

DAY FIVE (12th April)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:30	Recap	day 4	LMF TEAM	Question sheets (!)
10:30	10:45	BREAK	BREAK	BREAK	note: break might have been too early? (usually in between the Optical sectioning talk)
10:45	13:00	SESSION 1 Theory & Demo	Optical sectioning methods Pros&Cons	JAN	"confocal equipment": laser pointer, mirror, broken scanning mirror dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength Pete's suitcase SPIM??
13:00	14:00	LUNCH	LUNCH	LUNCH	Optional: LMF tour
14:00	14:10	SESSION 2	Planning your Imaging Experiment	DAVIDE
14:10	15:15	SESSION 3 Project discussion	Selected (volunteering) users present their imaging problems shortly and discuss it with the whole group	LMF TEAM	NOTE: this is an experiment: if no user is volunteering to present in front of the whole group, we'll switch back to the old format of small group project discussions
15:15	16:00	SESSION 3	Course evaluation	LMF TEAM