BasicCoursePhDProg - Peter Evennett - schedule March 2015
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PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course March 2015
SETUP - Thu 12th and Fri 13th March
Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Thu
Part of teaching microscopes where already set up before for the TA course
Setup of all needed course material in Galeria on Fri starting 9AM
Equipment needed
- 10 tables
- Microscopes (6 teaching stations, 1 demo station, Peter's diffraction demo scope)
- cell culture microscope
- stereo microscope with coin
- Optical bench
- Spinning disk gadget
- Polarizing sheets
- Diffraction Grids
- Sample map for each teaching station with: diatomes, liver tissue, Convolaria, Benzocain crystals
- microscope handout booklet for each teaching station
- First day handout for students
- Light torches
- Cameras and lab-tops for teaching stations
- Cleaning stations for each system containing: cover slips, slides, Qtips, water, 70% EtOH, lens cleaning tissue, EDTA, immersion oil, nail polish
- Waste and glass waste for each teaching station
- Box with screw drivers (1x 3mm, 2x 1.5mm), telescope, eye pieces, microscope ruler, mirror slide, DIC objective and Wollaston prism for each microscope
- 2 small polarization filter sheets for each microscope
- Box with red, green, blue, black board marker, pen, pencil, sharpener, ruler, calculator for each microscope
DAY ONE - Mon 16th March
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
8:30 | 09:00 | FINAL PREP | Test everything works | BioDIP TEAM | |
9:00 | 9:38 | INTRODUCTION | COURSE INTRO WHO is WHO? Round table |
BioDIP TEAM | White board and pen; ask students for volunteering for Friday's project discussion round |
9:38 | 10:35 | Session 1 Theory |
PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles (incl. refraction and resolution basics) |
PETER EVENNETT (BioDIP TEAM) | students shortly watch airy pattern from hole in mirror at the teaching microsopes (~10:08 - 10:15) |
10:35 | 10:50 | BREAK | BREAK | ||
10:50 | 11:35 | SESSION 1 Practice 3 groups, 12min Rotation (+3min for switching stations) Timer: SEBASTIAN |
capillary/plastic (Huisken) in oil demo Coin-in-cup demo red, green laser through water bath - measure angles, calculate refraction; show immersion objectives measure refraction with modern refractometer |
JAN BRITTA DAVIDE |
*capillaries, oil * coin-in-cup, water, beaker for water * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and water, laminated image of ice bear in water/air *water, glycerol, oil immersion objectives *refractometer |
11:35 | 12:15 | SESSION 1 Theory |
Introduction to lenses and objectives Numerical aperture Magnification |
PETER EVENNETT | cut objectives |
12:15 | 13:05 | LUNCH | LUNCH | ||
13:05 | 13:52 | SESSION 1 Practice 15min (!) Rotation Timer: Sebastian |
Milky Glass Block demo Show and discuss microscope parts (upright and inverted) NA measurements |
JAN/DAVIDE 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 |
13:52 | 14:50 | SESSION 2 Theory |
Microscope illumination Conjugate planes Apertures |
PETER EVENNETT | |
14:50 | 15:05 | BREAK | BREAK | ||
15:05 | 16:05 | SESSION 2 Practice (30min Rotation inlc. time for switching) Timer: SEBASTIAN |
conjugate planes on Peters microscope conjugate planes on optical bench + effect of changing field and aperture diaphragms on demo scope |
PETER EVENNETT JAN |
*Peters microscope setup *optical bench demonstrating a transmitted light microscope, incl. light source conjugate planes scheme hand outs |
16:05 | 16:40 | SESSION 3 Theory |
Koehler illumination Epi illumination (Microscope alignment) |
PETER EVENNETT | |
16:30 | 17:30 | SESSION 3 Practice |
Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
17:30 | 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 - Tue 17th March
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:10 | Recap | day 1 | BioDIP TEAM | Questions teaching microscopes; conjugate planes schemes |
10:10 | 11:05 | SESSION 1a DEMONSTRATION + THEORY |
Diffraction and Diffraction slide fun Diffraction string show Diffraction and Resolution |
PETER EVENNETT | diffraction slides, torch, "dashed" string, fabric, funny glasses |
11:05 | 11:20 | BREAK | COFFEE BREAK |
| |
11:20 | 11:50 | SESSION 1b Demo and Theory |
ABBE's diffraction demonstration | BERT | Dan's ABBE Diffraction demo setup |
11:50 | 12:20 | SESSION 1b Practice |
Diffraction hands on on student microscopes | BioDIP TEAM | gratings, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm, some small scissors would be nice |
12:20 | 13:00 | SESSION 1b Demo and Theory |
Peter's Diffraction video (w/o parts on Dark field and Phase contrast!) | JAN (PETER EVENNETT) |
video |
13:00 | 14:00 | BREAK | LUNCH | ||
14:00 | 14:15 | SESSION 1b Theory |
Wrap - up & Q & A Diffraction |
PETER EVENNETT JAN |
|
14:15 | 15:10 | SESSION 2 Theory and Demo |
Lens abERRations and corrections objective labeling/reading |
PETER EVENNETT JAN |
lenses with various sizes and shapes magnetic lens + laser suitcase on white board (15:05 - 15:10) |
15:10 | 15:15 | SHORT BREAK | FRESH AIR | ||
15:15 | 15:45 | SESSION 3 Theory |
Introduction to contrast | PETER EVENNETT | |
15:45 | 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 | 16:20 | SESSION 3a Theory |
Dark Field microscopy | PETER EVENNETT | Zeiss reflection dark field condenser from W3 + new 100x iris objective |
16:20 | 16:50 | SESSION 3a Practice |
Dark Field microscopy | BioDIP TEAM | diatom slides; cells/Chlamy's from Gaia; samples out of Ruth's Hay infusion |
16:50 | 17:00 | SESSION 3b Video |
Peter's Phase contrast diffraction video part | JAN (PETER EVENNETT) |
video |
17:00 | 17:20 | SESSION 3b Theory |
Basics of Phase Contrast microscopy | PETER EVENNETT | |
17:20 | 17:25 | SESSION 3b Demonstration |
Cheek cell prep | JAN | Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
17:25 | 18:10 | SESSION 3b Practice |
Phase Contrast microscopy | BioDIP TEAM | cheek cell samples |
DAY THREE - Wed 18th March
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:10 | Recap | day 2 | BioDIP TEAM | example you tube videos on dark field and phase contrast (9:05-9:10) Questions, pair of sieves, torches, microscopes |
10:10 | 10:45 | SESSION 1 Theory |
Objective reading lateral vs angular magnification |
PETER EVENNETT JAN |
objectives, eyepieces, overhead projector |
10:45 | 11:00 | BREAK | BREAK | BREAK | |
11:00 | 12:10 | SESSION 1 Practice Group rotation (30min each) |
Cover glasses, sample mounting, Objective cleaning and infinity optics bench demo Objective reading |
JAN BRITTA |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter bench demo of infinity optics box with broken objectives + two 160 tube lens objectives cell culture microscope with finite tube length |
12:10 | 13:00 | SESSION 2 Theory |
Polarized light microscopy | PETER EVENNETT | for students and Peter: calcite crystal blocks, polarizers, paper with black spot; overhead projector |
13:00 | 14:00 | BREAK | LUNCH | ||
14:00 | 14:05 | SESSION Meet & Greet |
Meeting Jean-Marc Verbavatz, Leader EM facility | JEAN-MARC (JAN) |
Q & A with Jean-Marc about his facility and cooperation with LMF |
14:05 | 14:45 | SESSION 2 Practice |
Polarized light microscopy | PETER EVENNETT BioDIP TEAM |
overhead projector, hair, stone samples, benzocain crystals, rulers, gummy bears, plastic dishes, ... |
14:45 | 15:10 | SESSION 3 Theory |
Differential Interference Contrast (DIC) | PETER EVENNETT | |
15:10 | 15:55 | SESSION 3 Practice |
Differential Interference Contrast (DIC) | BioDIP TEAM JAN |
cheek cell samples, diatoms |
15:55 | 16:10 | BREAK | BREAK | BREAK | |
16:10 | 16:30 | Question round | Questions to Peter Evennett | PETER EVENNETT BioDIP TEAM |
questions to Peter; DIC video from web and Britta's moving keratocytes (16:15 - 16:20) remind students on Friday's project discussion round |
16:30 | 17:05 | SESSION 3 Theory |
Fundamental concepts of fluorescence | JAN BRITTA |
fluorescent liquids in bottles plus laser pointer (blue, green, red; need stronger red + green ones!) |
17:05 | 18:00 | SESSION 4 Theory |
Introduction to fluorescence microscopy and light sources |
DAVIDE JAN |
• Light sources • Lamp houses |
19:00 | open end | Dinner | with Peter | BioDIP TEAM | good mood, time |
DAY FOUR - Thu 19th March
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | DEMO Activities | Materials needed |
9:00 | 10:10 | Recap | day 3 | BioDIP TEAM | - | Questions |
10:10 | 10:50 | SESSION 1 Theory |
2nd part Fluorescence Microscopy | DAVIDE JAN |
- | Spectra Filters Filter cubes |
10:50 | 11:05 | SESSION 1 Practice |
Filters | BioDIP TEAM | - | laminated sheets with grids for spectra drawing red, green, blue, black board markers EtOH spray bottles, tissue |
11:05 | 11:20 | BREAK | BREAK | BREAK | BREAK | BREAK |
11:20 | 12:25 | SESSION 1 Practice |
Spectraviewer Aligment of Mercury arc lamps Fluorescence imaging at microscopes |
JAN BioDIP TEAM |
- | lamp house, screw driver laminated sheets with DAPI/FITC/TRITC Spectra red, green, blue, board markers EtOH spray bottles + tissue Fluorescent labeled samples (Convallaria) |
12:25 | 12:35 | SESSION 1 Theory |
Chromatic Aberration Correction | DAVIDE | - | |
12:35 | 13:15 | SESSION 2 Theory |
Detectors | BRITTA | - | CCD chip paper weight Demo: CCD chip under stereo microscope example cameras showing different chip sizes |
13:15 | 14:00 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
14:00 | 14:30 | SESSION 2 Demo & Theory |
Detectors | BRITTA | bench show advacned detectors lecture |
RT spot with RGB slider and camera objective PC nice sample for binning (coffee cup) |
14:30 | 14:35 | SESSION 2 Practice |
Detectors "QE" show |
JAN | students count times of laser pointer blinking | blinking laser pointer |
14:35 | 15:00 | SESSION 3a Theory & Demo |
Digital images | BERT JAN |
Nyquist-Shannon what is a pixel spatial calibration |
overhead projector sheets with different sized squares as example for dexel size gummi bears, Sesame seeds |
15:00 | 15:35 | SESSION 3 Practice |
calculating dexel/pixel size | BioDIP TEAM | practice calculating needed dexel size for given optical setup | calculator text with given optical setup (within Bert's presentation) |
15:35 | 15:50 | SESSION 3b Theory |
Quantitative Imaging | BERT | digitization in space, time & intensity aliasing |
- |
15:50 | 16:05 | BREAK | BREAK | |||
16:05 | 17:15 | SESSION 4 Practice |
discussion and practice imaging with CCD/CMOS cameras on student microscopes | BioDIP TEAM | check out basic camera vocabulary discussing spec sheets of student microscope cameras spatial calibration with ruler and FIJI LUT, saturation, histogram etc |
camera spec sheets (in microscope handbook at each teaching scope) Hamamatsu camera comparison list (extra sheet) camera vocabulary checklist (in microscope handbook at each teaching scope) microscope ruler Fluorescence Sample slides (Kidney / Cells...) |
17:15 | 17:20 | SESSION Meet & Greet |
Meeting Marc Bickle, leader of Screening facility | MARC (JAN) |
Q & A with Marc about his facility and cooperation with LMF | |
17:20 | 18:00ish open end |
SESSION 4 Practice |
finish practice discussion from before | LMF TEAM | show to whole group: BioDIP Wiki with pages for all BioDIP systems |
offer LMF tour for Monday afternoon find out who would be interested |
DAY FIVE - Fri 20th March
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:00 | Recap | day 4 | BioDIP TEAM | Question sheets with the real case problem 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 | 11:40 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING Laser Scanning Confocal 2PM |
JAN SEBASTIAN |
"confocal equipment": laser pointer, mirror, broken scanning mirror dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength |
11:40 | 12:25 | SESSION 1c Theory & Demo |
OPTICAL SECTIONING Spinning disc confocal TIRF SPIM |
JAN BRITTA DAVIDE |
* DAN's "spinning-disc-on-a-bench" * small glass cube with olive oil over milky water (use more oil than water!) plus Dan's blue laser pointer * glass block with brain/scull and red light sheet laser from ZEISS |
12:25 | 12:35 | SESSION 1c Demo |
OPTICAL SECTIONING SPIM |
PETE | PETE's SPIM-in-a-suitcase |
12:35 | 12:45 | SESSION 1d Theory |
OPTICAL SECTIONING Apotome |
JAN | |
12:45 | 13:30 | LUNCH | LUNCH | LUNCH | |
13:30 | 13:45 | SESSION 1e Theory |
OPTICAL SECTIONING final remarks |
JAN | |
13:45 | 14:10 | SESSION 1f Theory |
SUPER-RESOLUTION SIM STORM |
BERT | |
14:10 | 14:20 | SESSION 2 | Planning your Imaging Experiment | DAVIDE | + introduction to new user project questions |
14:20 | 15:00 | SESSION 3 Project discussion |
Two volunteers present their imaging problems shortly and discuss it with the whole group | BioDIP TEAM + BENOIT |
NOTE: ask for volunteers already on Monday, than again on Wednesday; |
15:00 | 16:00 | SESSION 3 | Course evaluation | BioDIP TEAM | Gummy bear bags and/or fruits white board + marker |