BasicsCoursePhDprog-PeterEvennett - schedule Oct. 2013
From BioDIP
Contents |
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 | LMF | |
9:00 | 9:35 | INTRODUCTION | COURSE INTRO WHO is WHO? Round table |
LMF 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 (LMF 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 this) |
12:10 | 13:00 | 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 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 |
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 (15th Oct)
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 | 12:15 | SESSION 2b Demo and Theory |
Dan's diffraction setup demonstration | BERT | Dan's ABBE Diffraction demo setup |
12:15 | 12:45 | SESSION 2b Practice |
Diffraction hands on on student microscopes | LMF TEAM | gratings, sieves, ... |
12:45 | 13:30 | BREAK | LUNCH | ||
13:30 | 14:15 | SESSION 2b Demo and Theory |
Peter's Diffraction video (w/o parts on Darkfield and Phase contrast!) | PETER | video |
14:15 | 15:00 | SESSION 3 Theory and Demo |
Lens aberrations and corrections | PETER EVENNETT JAN |
magnetic lens + laser suitcase on white board| |
15:00 | 15:30 | SESSION 4 Theory |
Introduction to contrast | PETER EVENNETT | |
15:30 | 15:45 | BREAK | COFFEE BREAK | ||
15:45 | 16:05 | SESSION 4a Theory |
Dark Field microscopy | PETER EVENNETT | |
16:05 | 16:15 | SESSION 4a Video |
Peter's Dark Field diffraction video part | PETER EVENNETT | |
16:15 | 16:40 | SESSION 4a Practice |
Dark Field microscopy | LMF TEAM | diatome slides |
16:40 | 17:00 | SESSION 4b Theory |
Basics of Phase Contrast microscopy | PETER EVENNETT | |
17:00 | 17:10 | SESSION 4b Video |
Peter's Phase contrast diffraction video part | PETER EVENNETT | |
17:10 | 17:50 | SESSION 4b Practice |
Phase Contrast microscopy | LMF TEAM | cheek cell samples |
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 | 12:45 | 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 | 17:15 | SESSION 3 Theory |
Fundamental concepts of fluorescence | JAN | fluorescent liquids in bottles plus laser pointer (blue, green, red) |
17:15 | 17:45 | SESSION 4 Theory |
Fluorescence microscopy introduction and light sources | DAVIDE | • Light sources • Lamp houses |
DAY FOUR (17th Oct)
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 |
2nd part Fluorescence Microscopy | DAVIDE | - | • Spectra • Filters • Filter cubes • Filter spectral charts of each microscope (laminated) |
10:45 | 11:00 | BREAK | BREAK | BREAK | BREAK | BREAK |
11:00 | 12:00 | SESSION 1 Practice |
Fluorescence imaging at microscopes | LMF TEAM | - | • Fluorescent labeled samples (Convallaria) |
12:00 | 13:00 | SESSION 2 Theory & Practice |
Detectors | BRITTA | • CCD chip • example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope |
|
13:00 | 14:00 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
14:00 | 14:30 | SESSION 2 Practice |
Basic camera "vocabulary" on students microscopes | LMF TEAM | - | checklist |
14:30 | 15:45 | SESSION 3 Theory |
What is a pixel Analog to Digital conversion Nuyquist-Shannon Quantitative Imaging Spatial Calibration |
BERT | - | • pixel size calculation on a given optical setup |
15:45 | 16:00 | BREAK | BREAK | |||
16:00 | 16:45 | SESSION 4a Practice |
camera discussion on student microscopes | LMF TEAM | • guidelines for choosing camera • spatial calibration • camera specs sheet discussion |
• camera specs sheets • checklist |
16:45 | 18:00 | SESSION 4b 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 (18th Oct)
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 |