BasicsCoursePhDprog-PeterEvennett - schedule March 2014
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Revision as of 12:09, 4 March 2014
Contents |
PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course March 2014
SETUP - Thu 13th and Fri 14th March
Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF on Thu
Setup of all needed course material in Galeria on Fri starting 12PM
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 - Mon 17th March
| 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, calculate refraction; show immersion objectives |
JAN BRITTA |
*capillaries, oil * coin-in-cup, water * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and milky water *water, glycerol, oil immersion objectives |
| 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 - Tue 18th March
| 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; cells from Gaia |
| 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 - Wed 19th March
| 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, 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 |
| 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 JAN |
cheek cell samples, diatoms DIC video from web (15:40 - 15:45) |
| 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 |
DAVIDE JAN |
• Light sources • Lamp houses |
DAY FOUR - Thu 20th March
| 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 | DAVIDE 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 images | 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 DAN BRITTA BERT DAVIDE |
to whole group: BioDIP Wiki with pages for all systesms at single stations: camera spec sheet of respective cameras LUT, saturation, histogram etc |
Microscopes: pDV of OMX (DAN, 2 students) N-Storm (BRITTA, 3 students) Oly-TIRF (BERT, 3 students) self-built-system (JAN, 3 students) DVcore (DAVIDE, 3 students) Fluorescence Sample slides (Kidney / Cells...) camera spec sheets of respective camera |
| 19:00 | open end | Dinner | with Peter | BioDIP TEAM | good mood, time |
DAY FIVE - Fri 21st 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 | 11:30 | 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 | 12:50 | SESSION 1e Theory |
SUPER-RESOLUTION SIM STORM |
BERT | |
| 12:50 | 13:45 | LUNCH | LUNCH | LUNCH | Optional: LMF tour |
| 13:45 | 14:00 | SESSION 2 | Planning your Imaging Experiment | DAVIDE | + introduction to new user project questions |
| 14:00 | 15:00 | 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 |
| 15:00 | 16:00 | SESSION 3 | Course evaluation | BioDIP TEAM | Gummy bear bags (last time it was apples :-)) white board + marker |
