BasicsCoursePhDprog-PeterEvennett - schedule Oct. 2013

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

SETUP - Fri 11th Oct

Setup of all needed course material in Galeria

Equipment needed

• Microscopes
• Optical bench
• Spinning disk gadget
• Polarizing sheets
• Diffraction Grids
• Sample map for each teaching station with: diatomes, liver tissue, convolaria, Benzocain crystals
• First day handout for students
• Light torches
• Cameras and labtops for teaching stations
• Cleaning stations for each system containing: cover slips, slides, Qtips, water, 70% EtOH, lens cleaning tissue
• Waste and glass waste for each table
• Box with screw drivers, telescope, eye pieces, ruler, mirror slide, DIC objective and wollaston prism for each microscope
• 2 polarization filters for each microscope
• Box with red, green, blue, black board marker, pen, pencil, sharpener, ruler, calculator for each microscope

DAY ONE (14th Oct)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
8:30	09:00	FINAL PREP	Test everything works	BioDIP TEAM
9:00	9:35	INTRODUCTION	COURSE INTRO WHO is WHO? Round table	BioDIP TEAM	White board and pen
9:35	10:32	Session 1 Theory	PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles (incl. refraction-basics)	PETER EVENNETT (BioDIP TEAM)	students shortly watch airy pattern from hole in mirror at the teaching microsopes (~10:05 - 10:10)
10:32	10:45	BREAK	BREAK
10:45	11:20	SESSION 1 Practice 2 groups, 15min Rotation	capillary/plastic (Huisken) in oil demo Coin-in-cup demo red, green, blue laser through milky water bath - measure angles, calc refraction	JAN BRITTA	*capillaries, oil * coin-in-cup, water * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and milky water
11:20	12:10	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 (did not do it this time)
12:10	13:00	LUNCH	LUNCH
13:00	13:55	SESSION 1 Practice 15min (!) Rotation (Isa watched the time)	Milky Glass Block demo Show and discuss microscope parts (upright and inverted) NA measurements	JAN BRITTA BERT	*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
13:55	14:45	SESSION 2 Theory	Magnification: lateral vs angular Microscope illumination Conjugate planes	PETER EVENNETT
14:45	15:05	BREAK	BREAK
15:05	16:10	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
16:10	16:45	SESSION 3 Theory	Koehler illumination Epi illumination (Microscope alignment)	PETER EVENNETT
16:45	17:45	SESSION 3 Practice	Koehler illumination (Microscope alignment)	BioDIP TEAM	students manual microscopes, screwdrivers, nice brightfield sample
17:45	18:00	SESSION 4 Theory & Practice	Eyepieces Depth of field Depth of focus	PETER EVENNETT BioDIP TEAM	students microscopes with 10x/0.25 and 40x/0.65 objectives Stereoscope with a "sample"

DAY TWO (15th Oct)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:10	Recap	day 1	BioDIP TEAM	Questions
10:10	11:05	SESSION 1a DEMONSTRATION	Diffraction and Diffraction slide fun Diffraction string show	PETER EVENNETT	diffraction slides, torch, "dashed" string, fabric, funny glasses
11:05	11:25	BREAK	COFFEE BREAK
11:25	11:55	SESSION 1b Demo and Theory	ABBE's diffraction demonstration	BERT	Dan's ABBE Diffraction demo setup
11:55	12:15	SESSION 1b Practice	Diffraction hands on on student microscopes	BioDIP TEAM	gratings, sieves, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm
12:15	12:50	SESSION 1b Demo and Theory	Peter's Diffraction video (w/o parts on Dark field and Phase contrast!)	JAN (PETER EVENNETT)	video
12:50	14:00	BREAK	LUNCH
14:00	14:10	SESSION 1b Theory	Wrap - up Diffraction	PETER EVENNETT JAN
14:10	15:10	SESSION 2 Theory and Demo	Lens abERRations and corrections	PETER EVENNETT JAN	magnetic lens + laser suitcase on white board (15:05 - 15:10)
15:10	15:35	SESSION 3 Theory	Introduction to contrast	PETER EVENNETT
15:35	16:00	BREAK	COFFEE BREAK
16:00	16:10	SESSION 3a Video	Peter's Dark Field diffraction video part	JAN (PETER EVENNETT)	video
16:10	16:15	SESSION 3a Theory	Dark Field microscopy	PETER EVENNETT
16:15	16:40	SESSION 3a Practice	Dark Field microscopy	BioDIP TEAM	diatom slides
16:40	16:50	SESSION 3b Video	Peter's Phase contrast diffraction video part	JAN (PETER EVENNETT)	video
16:50	17:00	SESSION 3b Theory	Basics of Phase Contrast microscopy	PETER EVENNETT
17:00	17:10	SESSION 3b Demonstration	Cheek cell prep	JAN	Q-tips, slides, cover slips, PBS, plastic pipette, nail polish
17:10	17:50	SESSION 3b Practice	Phase Contrast microscopy	BioDIP TEAM	cheek cell samples; you tube phase contrast video

DAY THREE (16th Oct)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:10	Recap	day 2	BioDIP TEAM	Questions, pair of sieves, torches, microscopes
10:10	10:30	SESSION 1 Theory	Objective reading	PETER EVENNETT JAN	objectives, eyepieces, overhead projector
10:30	10:55	BREAK	BREAK	BREAK
10:55	12:10	SESSION 1 Practice Group rotation	Cover glasses, sample mounting and Objective cleaning Objective reading	JAN BRITTA	Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter box with broken objectives + two 160 tube lens objectives
12:10	12:50	SESSION 2 Theory	Polarized light microscopy	PETER EVENNETT
12:50	13:55	BREAK	LUNCH
13:55	14:40	SESSION 2 Practice	Polarized light microscopy	PETER EVENNETT BioDIP TEAM	overhead projector, hair, stone samples, benzocain crystals, rulers, gummy bears, plastic dishes, ...
14:40	15:05	SESSION 3 Theory	Differential Interference Contrast (DIC)	PETER EVENNETT
15:05	15:45	SESSION 3 Practice	Differential Interference Contrast (DIC)	BioDIP TEAM	cheek cell samples, diatoms
15:45	16:00	BREAK	BREAK	BREAK
16:00	16:20	Question round	Questions to Peter Evennett	PETER EVENNETT BioDIP TEAM
16:20	17:00	SESSION 3 Theory	Fundamental concepts of fluorescence	JAN	fluorescent liquids in bottles plus laser pointer (blue, green, red)
17:00	18:00	SESSION 4 Theory	Introduction to fluorescence microscopy and light sources	BRITTA JAN	• Light sources • Lamp houses
19:30	open end	Dinner	with Peter	BioDIP TEAM

DAY FOUR (17th Oct)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	DEMO Activities	Materials needed
9:00	10:05	Recap	day 3	BioDIP TEAM	-	Questions
10:05	10:50	SESSION 1 Theory	2nd part Fluorescence Microscopy	BRITTA JAN	-	Spectra Filters Filter cubes
10:50	11:00	SESSION 1 Practice	Filters	BioDIP TEAM	-	laminated sheets with grids for spectra drawing red, green, blue, black board markers EtOH spray bottles, tissue
11:00	11:20	BREAK	BREAK	BREAK	BREAK	BREAK
11:20	12:15	SESSION 1 Practice	Fluorescence imaging at microscopes	BioDIP TEAM	-	laminated sheets with DAPI/FITC/TRITC Spectra red, green, blue, board markers EtOH spray bottles + tissue Fluorescent labeled samples (Convallaria)
12:15	12:55	SESSION 2 Theory	Detectors	BRITTA	-	CCD chip paper weight example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope (for later)
12:55	13:50	BREAK	LUNCH	LUNCH	LUNCH	LUNCH
13:50	14:20	SESSION 2 Demo & Theory	Detectors	BRITTA	bench show advacned detectors lecture	RT spot with slider and camera objective PC nice sample for binning
14:20	14:25	SESSION 2 Practice	Detectors "QE" show	JAN	students count times of laser pointer blinking	blinking laser pointer
14:25	14:50	SESSION 3a Theory	Digital sampling	BERT	Nyquist-Shannon what is a pixel spatial calibration	-
14:50	15:05	SESSION 3 Practice	calculating dexel/pixel size	BioDIP TEAM	practice calculating needed dexel size for given optical setup	calculator text with given optical setup
15:05	15:25	SESSION 3b Theory	Quantitative Imaging	BERT	digitization in space, time & intensity aliasing	-
15:25	15:45	BREAK	BREAK
15:45	16:55	SESSION 4a+b Practice	camera discussion on student microscopes	BioDIP TEAM	check out basic camera vocabulary discussing spec sheets of student microscope cameras spatial calibration with ruler and FIJI	camera spec sheets Hamamatsu camera comparison list camera vocabulary checklist microscope ruler
16:55	18:00ish open end	SESSION 4c Practice	Imaging with CCD cameras using LMF systems	JAN BRITTA BERT	camera spec sheet of respective cameras LUT, saturation, histogram etc BioDIP Wiki	Microscopes: N-Storm (BRITTA, 4 students) W1 Oly-TIRF (BERT, 3 students) self-built-system (JAN, 4 students)) Fluorescence Sample slides (Kidney / Cells...) camera spec sheets of respective camera

DAY FIVE (18th Oct)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)	Materials needed
9:00	10:00	Recap	day 4	BioDIP TEAM	Question sheets calculators, pens
10:00	10:30	SESSION 1a Theory	OPTICAL SECTIONING introduction widefield & deconvolution chromatic aberration & correction	JAN	labtop
10:30	10:45	BREAK	BREAK	BREAK
10:45	11:30	SESSION 1b Theory & Demo	OPTICAL SECTIONING Laser Scanning Confocal 2PM	JAN BRITTA	"confocal equipment": laser pointer, mirror, broken scanning mirror dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength
11:30	12:15	SESSION 1c Theory & Demo	OPTICAL SECTIONING Spinning disc confocal TIRF SPIM	BRITTA JAN	DAN's "spinning-disc-on-a-bench" small glass cube with olive oil over milky water plus 5mW blue laser pointer (CRTD) glass block with brain/scull and red light sheet laser from ZEISS
12:15	12:30	SESSION 1c Demo	OPTICAL SECTIONING SPIM	PETE	PETE's SPIM-in-a-suitcase (on a bench this time) glass block with whole scull PETE's light sheet laser from whicked laser
12:30	12:40	SESSION 1d Theory	OPTICAL SECTIONING Apotome final remarks	JAN
12:40	13:45	LUNCH	LUNCH	LUNCH	Optional: LMF tour
13:45	14:00	SESSION 2	Planning your Imaging Experiment	BERT	+ introduction to new user project questions
14:00	14:50	SESSION 3 Project discussion	Three volunteer users present their imaging problems shortly and discuss it with the whole group	BioDIP TEAM	NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low
14:50	15:50	SESSION 3	Course evaluation	BioDIP TEAM	Gummy bear bags (last time it was apples :-)) white board + marker
15:50	16:00	SESSION 4	Introduction to BioDIP Wiki	BRITTA	lab top