BasicCoursePhDProg - Peter Evennett - schedule April 2016
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Revision as of 12:28, 13 April 2016
Contents |
PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course April 2016
Tentative Schedule
SETUP - Wed and Thu April (Fri TA course)
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 Thu starting 9AM
Equipment needed
- 10 tables (we need to order them early on - Davide will do; for Wed evening)
- Microscopes (6 teaching stations, 1 demo station, Peter's diffraction demo scope) (we will try to order another microscope body)
- cell culture microscope (normally with EM people; currently moved to cell culture room 4th floor south; Jan knows and will take care of getting it for the course)
- stereo microscope with coin (currently broken; Bert will take care of getting it repaired)
- 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 18th April
| 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 (we need four volunteers) |
| 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 | 16:35 | SESSION 3 Theory |
Koehler illumination Epi illumination (Microscope alignment) |
PETER EVENNETT | |
| 16:35 | 17:35 | SESSION 3 Practice |
Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
| 17:35 | 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 19th April
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 10:05 | Recap | day 1 | BioDIP TEAM | Questions teaching microscopes; conjugate planes schemes |
| 10:05 | 11:00 | 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 if available: wave/ripple tank; interferometer |
| 11:00 | 11:15 | BREAK | COFFEE BREAK |
| |
| 11:15 | 11:45 | SESSION 1b Demo and Theory |
ABBE's diffraction demonstration | BERT | Dan's ABBE Diffraction demo setup |
| 11:45 | 12:25 | SESSION 1b Practice |
Diffraction hands on on student microscopes | BioDIP TEAM | rulers as gratings, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm, some small scissors would be nice |
| 12:25 | 12:35 | SESSION 1c Theory |
Wrap - up & Q & A Diffraction |
PETER EVENNETT JAN |
|
| 12:35 | 13:30 | BREAK | LUNCH | ||
| 13:30 | 14:25 | 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 (14:15 - 14:25) |
| 14:25 | 15:00 | SESSION 3 Theory |
Objective reading lateral vs angular magnification |
PETER EVENNETT JAN |
objectives, eyepieces, overhead projector |
| 15:00 | 15:05 | QUESTION ROUND | questions to Peter Evennett | PETER EVENNETT | |
| 15:05 | 15:35 | SESSION 3 Practice Round 1 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 |
| 15:35 | 15:50 | BREAK | COFFEE BREAK | ||
| 15:50 | 16:20 | SESSION 3 Practice Round 2 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 |
| 16:20 | 16:35 | SESSION 4 Theory |
Introduction to contrast | BERT | |
| 16:35 | 16:50 | SESSION 5a Theory |
Basics of Dark Field microscopy | JAN | Zeiss reflection dark field condenser from W3 + new 100x iris objective video with dark field example; from web and own |
| 16:50 | 17:20 | SESSION 5b Practice |
Dark Field microscopy | BioDIP TEAM | diatom slides |
| 17:20 | 17:40 | SESSION 6a Theory |
Basics of Phase Contrast microscopy | DAVIDE | including videos from web and own |
| 17:40 | 18:10 | SESSION 6b Practice |
Phase Contrast microscopy | BioDIP TEAM | diatomes and similar samples cell culture microscope with cells in a dish as live example for phase contrast |
| 19:00 | open end | Dinner | with Peter | BioDIP TEAM | good mood, time |
DAY THREE - Wed 20th April
| 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 Demonstration |
Polarized light microscopy | SEBASTIAN JAN |
for students and Sebastian: calcite crystal blocks, polarizers, paper with black spot; overhead projector stone samples, gummy bears, plastic dishes, plastic rulers... |
| 10:30 | 11:00 | SESSION 1 Theory |
Polarized light microscopy | SEBASTIAN | info about LC-PolScope from openpolscope.org/ introduce responsible person for Brugues' PolScope |
| 11:00 | 11:15 | BREAK | BREAK | BREAK | |
| 11:15 | 11:45 | SESSION 1 Practice |
Polarized light microscopy | BioDIP TEAM | hair, stone samples, benzocain crystals, tissue pieces ... |
| 11:45 | 12:05 | SESSION 2 Theory |
Differential Interference Contrast (DIC) | BRITTA | |
| 12:05 | 12:10 | SESSION 2 Demonstration |
Cheek cell prep | JAN | Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
| 12:10 | 13:00 | SESSION 2 Practice |
Differential Interference Contrast (DIC) | BioDIP TEAM JAN |
cheek cell samples, diatoms |
| 13:00 | 14:00 | BREAK | LUNCH | ||
| 14:00 | 14:05 | SESSION Meet & Greet |
Meeting Mark Bickle, Leader Technology development studio screening facility |
MARK (JAN) |
Q & A with Mark about his facility |
| 14:05 | 14:30 | Wrap-up compare methods |
Transmitted light contrasting techniques | BERT BioDIP TEAM |
first comparison than Quiz with various videos of the different techniques; remind students on Friday's project discussion round |
| 14:30 | 15:15 | SESSION 3 Theory |
Fundamental concepts of fluorescence | JAN | fluorescent liquids in bottles plus laser pointer (blue, green, red; need stronger red + green ones!) (in seminar room for darkness) |
| 15:15 | 15:45 | SESSION 4a Theory |
Introduction to fluorescence microscopy and light sources |
DAVIDE JAN |
• Light sources • Lamp houses |
| 15:45 | 16:00 | BREAK | BREAK | BREAK | |
| 16:00 | 16:15 | SESSION 4b Theory |
Introduction to fluorescence microscopy and light sources ctd. |
DAVIDE JAN |
• Light sources • Lamp houses |
| 16:15 | 16:55 | SESSION 4c Theory |
Introduction to fluorescence microscopy Filters, spectra etc. |
DAVIDE JAN |
Spectra Filters Filter cubes |
| 16:55 | 17:10 | SESSION 4d Practice |
Filters | BioDIP TEAM | laminated sheets with grids for spectra drawing red, green, blue, black board markers EtOH spray bottles, tissue |
| 17:10 | 18:15 | SESSION 4e 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 (Convalaria) |
DAY FOUR - Thu 21st April
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | DEMO Activities | Materials needed |
| 9:00 | 10:05 | Recap | day 3 | BioDIP TEAM | - | Questions (need to be adjusted to new course scheme!) |
| 10:05 | 10:30 | SESSION 1 Theory |
Fluorophores | DAVIDE SEBASTIAN |
- | |
| 10:30 | 11:10 | SESSION 2 Theory |
Detectors | BRITTA | - | CCD chip paper weight Demo: CCD chip under stereo microscope example cameras showing different chip sizes |
| 11:10 | 11:25 | BREAK | BREAK | BREAK | BREAK | BREAK |
| 11:25 | 12:10 | 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) |
| 12:10 | 12:15 | SESSION 2 Practice |
Detectors "QE" show |
JAN | students count times of laser pointer blinking | blinking laser pointer |
| 12:15 | 12:55 | 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 |
| 12:55 | 13:45 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
| 13:45 | 13:55 | SESSION Meet & Greet |
Meeting Tobias Fürstenhaupt, Leader EM facility | Tobias (JAN) |
Q & A with Tobias about his facility and cooperation with LMF | - |
| 13:55 | 14:15 | SESSION 3a 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) |
| 14:15 | 14:25 | SESSION 3a Practice |
calculating dexel/pixel size | BERT | practice calculating needed dexel size for given optical setup | evaluation of the results from practical plus more calculation examples |
| 14:25 | 14:50 | SESSION 3b Theory |
Quantitative Imaging | BERT | digitization in space, time & intensity aliasing |
- |
| 14:50 | 15:50 | 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...) |
| 15:50 | 16:05 | BREAK | BREAK | |||
| 16:05 | 16:35 | SESSION 5a Theory |
OPTICAL SECTIONING introduction widefield & deconvolution |
JAN | - | labtop |
| 16:35 | 16:45 | SESSION 6 Theory |
CHROMATIC ABERRATION | SEBASTIAN | ||
| 16:45 | 17:05 | SESSION 5b Theory & Demo |
OPTICAL SECTIONING Laser Scanning Confocal |
JAN | "confocal equipment": laser pointer, mirror, broken scanning mirror | |
| 17:05 | 17:25 | SESSION 5c Theory& Demo |
OPTICAL SECTIONING 2-Photon Microscopy |
SEBASTIAN JAN |
dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength | |
| 17:25 | 17:45 | SESSION 5d Theory |
OPTICAL SECTIONING Spinning Disc Confocal |
BRITTA | beer bottle from Plzen laminated sheets and copies of Nipkow's and Petran's patents | |
| 17:45 | 18:00 | SESSION 5d Demo |
OPTICAL SECTIONING Spinning Disc Confocal |
JAN | DAN's "spinning-disc-on-a-bench" |
DAY FIVE - Fri 22nd April
| 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 voting kit? |
| 10:00 | 10:20 | SESSION 1a Theory & Demo |
OPTICAL SECTIONING TIRF |
BRITTA | small glass cube with olive oil over milky water (use more oil than water!) plus Dan's blue laser pointer |
| 10:20 | 10:40 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING SPIM |
DAVIDE | glass block with brain/scull and red light sheet laser from ZEISS |
| 10:40 | 11:00 | BREAK | BREAK | ||
| 11:00 | 11:15 | SESSION 1c Demo |
OPTICAL SECTIONING SPIM |
????? | PETE's SPIM-in-a-suitcase |
| 11:15 | 11:25 | SESSION 1d Theory |
OPTICAL SECTIONING Apotome |
JAN | |
| 11:25 | 11:40 | SESSION 1e Theory |
OPTICAL SECTIONING final remarks |
JAN | |
| 11:40 | 12:30 | SESSION 2 Theory |
SUPER-RESOLUTION SIM STORM STED Airyscan Sample Preparation |
BERT | with Olli from Honigman-lab? |
| 12:30 | 13:30 | LUNCH | LUNCH | LUNCH | |
| 13:30 | 13:35 | SESSION Meet & Greet |
Meeting Benoit Lombardot, Leader Scientific Computing facility | BENOIT (JAN) |
Q & A with Benoit about his facility and cooperation with LMF |
| 13:35 | 13:45 | SESSION 3 | Planning your Imaging Experiment | DAVIDE | + introduction to new user project questions |
| 13:45 | 14:45 | SESSION 4 Project discussion |
Four 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; (need more time next time) |
| 14:45 | 15:00 | SESSION 5 Practice |
BioDIP Wiki | LMF TEAM | show to whole group: BioDIP Wiki with pages for all BioDIP systems |
| 15:00 | 16:00 | SESSION 6 | Course evaluation | BioDIP TEAM | Gummy bear bags and/or fruits white board + marker |
DAY SIX - optional - Mon 25th April afternoon
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 12:00 | 13:00 | LUNCH | LUNCH | LUNCH | |
| 13:00 | 13:45 | Preparation for hands-on | OPTICAL SECTIONING / SUPER-RESOLUTION | BioDIP team | MZ1, LZ2, new LSM 880 inverted, SD4, D4, H1, H2 we need to decide which systems to use |
| 13:45 | 14:00 | Meeting students at switchboard |
OPTICAL SECTIONING / SUPER-RESOLUTION | BioDIP team | sign-up sheets for both hands-on sessions students decide which two systems (one per session) they want to get to know distribute students into groups |
| 14:00 | 15:30 | SESSION I hands-on |
OPTICAL SECTIONING / SUPER-RESOLUTION | BioDIP team | MZ1, LZ2, new LSM 880 inverted, SD4, D4, H1, H2 |
| 15:30 | 16:00 | BREAK | COFFEE | KATJA | |
| 16:00 | 17:30 | SESSION II hands-on |
OPTICAL SECTIONING / SUPER-RESOLUTION | BioDIP TEAM | MZ1, LZ2, new LSM 880, SD4, H1, H2 |
