BasicCoursePhDProg - Basics in Light Microscopy - schedule June 2022
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Revision as of 18:22, 25 July 2022
Contents |
PhD Program: Basics of Light Microscopy - LMF - Course June 2022
Tentative Schedule
SETUP - Thu June 23rd and Fri June 24th
Again in CSBD SR top floor, also using landing in front of it
+ 2 neighbouring offices + terrace
Room will be reserved from (incl) Thu, June 23rd 2022 9:00AM - Friday, July 1st, 6PM!
We need to confer with building maintenance to put back all tables and chairs whether Friday afternoon is enough time for them to do this
Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Wed June 22nd
Setup of all needed course material in CSDB SR top floor Thurs afternoon and Friday morning, can already start We afternoon/ Thu morning
Refreshments are organised by the PhD office (Reni)
Equipment needed
- printed out elaborate schedules for teachers
- slides online
- printed out coarse course schedule with QR code with link to slides location for students
- course handout for students - choice of online and/or printed (4)
- booklets Microscopy from the beginning by Zeiss
- 10 tables (do not need to order them, should be enough tables in the room)
- Microscopes (6 teaching stations, 1 demo station, Peter's diffraction demo scope)
- cell culture microscope
- stereo microscope with coin
- microscope stand with rotatable stage to demonstrate polarized light microscopy
- Optical bench
- Spinning disk gadget
- Overhead projector with digital source switch
- black board
- standing white board (CSBD)
- FITC in PBS in 3 x T-75 cell, 2 x T-25 culture flasks
- extra PBS bottle
- extra water bottle
- Polarizing sheets
- Diffraction Grids
- Sample map for each teaching station with: diatomes, liver tissue, Convolaria, tounge tissue, Benzocaine crystals, skull samples (get from Tabler lab); (check content of all)
- microscope handout booklet for each teaching station
- Flash lights (check batteries!)
- Cameras and lab-tops for teaching stations
- Cleaning stations for each system containing: cover slips, slides, Q-tips, water, 70% EtOH, lens cleaning tissue, PBS, immersion oil, nail polish (need to check carefully whether everything needed is there!)
- Waste and glass waste for each teaching station
- 70% EtOH spray bottle, tissue, and kitchen towels 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, small scissors for each microscope, (need to check carefully whether everything needed is there!)
DAY ONE - Mon 27th June
organize pitchers with water and cups for the short breaks
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
8:30 | 09:00 | FINAL PREP | Test everything works | BioDIP TEAM | put mirror slide with hole on each teaching station |
9:00 | 9:05 | INTRODUCTION | GENERAL OVERVIEW | JAN | |
9:05 | 9:25 | INTRODUCTION | COURSE INTRO WHO is WHO? Round table |
BioDIP TEAM | White board and pen |
9:25 | 09:45 | Session 1a Theory |
PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles (incl. refraction basics) |
JAN | |
09:45 | 09:55 | SESSION 1a Practice |
students watch Airy pattern from hole in mirror | BioDIP team | mirror slides with hole on each teaching station |
09:55 | 10:05 | Session 1b Theory |
PRINCIPLES OF LIGHT MICROSCOPY resolution basics |
BRITTA | |
10:05 | 10:20 | Session 1c Theory |
PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles |
JAN | |
10:20 | 10:30 | BREAK | BREAK | ||
10:30 | 11:15 | SESSION 1b Practice 3 groups, 15min Rotation (12min at stations + 3min for switching in-between) Timer: CATARINA |
capillary/plastic (Huisken) in oil demo Coin-in-cup demo hyrdogel spheres in water; red, green laser through water bath - measure angles, calculate refraction; show immersion objectives measure refraction with modern refractometer |
JAN BRITTA SEBASTIAN |
*capillaries, oil * water and oil tanks with glass rods from Anatol * coin-in-cup, water, beaker for water * hydrogel spheres, water beaker, glass container with big opening and lid * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and FITC-PBS solution, laminated image of ice bear in water/air *water, glycerol, oil immersion objectives (take from Tuesday box!) *refractometer & water, glycerol, regular oil & 2 clearing solutions (watery, glycerol-based) as unknowns |
11:15 | 11:40 | SESSION 1d Theory |
Introduction to lenses and objectives Magnification |
JAN | cut objective foam objective |
11:40 | 11:45 | SESSION 1e Demonstration |
Introduction to lenses and objectives Numerical aperture |
SEBASTIAN | draw pizza on white/black board (pizza or cake) |
11:45 | 12:45 | LUNCH | LUNCH | ||
12:45 | 13:30 | SESSION 1c Practice 3 groups, 15min Rotation (12min at stations + 3min for switching in-between) Timer: RICCARDO |
Milky Glass Block demo Show and discuss microscope parts (upright and inverted) NA measurements |
JAN BRITTA CATARINA |
*milky glass block, T-75 with FITC, teaching microscope, colored 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 |
13:30 | 14:05 | SESSION 2 Theory |
Microscope illumination Conjugate planes Apertures |
JAN | |
14:05 | 14:15 | BREAK | BREAK | ||
14:15 | 15:25 | SESSION 2 Practice 2 groups, 30min Rotation (27min at stations + 3min for switching in-between) Timer: RICCARDO |
conjugate planes on Peters microscope conjugate planes on optical bench + effect of changing field and aperture diaphragms on demo scope |
BRITTA JAN |
*Peters microscope setup with artificial eye ball *optical bench demonstrating a transmitted light microscope, incl. light source * conjugate planes scheme hand outs |
15:25 | 15:45 | SESSION 3 Theory |
Koehler illumination (Microscope alignment) |
JAN | |
15:45 | 16:00 | BREAK | BREAK | ||
16:00 | 17:15 | SESSION 3a Practice |
Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
17:15 | 17:20 | SESSION 4 Theory & Practice |
Eyepieces Depth of field Depth of focus more Koehler |
BRITTA BioDIP TEAM |
students microscopes with 10x/0.25 and 40x/0.65 objectives Stereoscope with a "sample" |
17:20 | 17:25 | SESSION 3b Practice |
finish Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
17:25 | 17:35 | SESSION 3 Theory |
Epi illumination | JAN | |
17:35 | 17:40 | Theory | Introduction to Peter Evennett's videos |
JAN | You tube videos |
19:00 | open end | Dinner - move to another day? | with all teachers | BioDIP TEAM | good mood, time |
DAY TWO - Tue 28th June
organize pitchers with water and cups for short breaks
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:00 | Feedback & Recap discussion in groups | day 1 | BioDIP TEAM | Update question list, ask for feedback teaching microscopes; conjugate planes schemes |
10:00 | 10:05 | BREAK | SHORT BREAK | ||
10:05 | 10:55 | SESSION 1a DEMONSTRATION |
Diffraction and Diffraction slide fun Diffraction string show |
JAN | diffraction slides, torch, "dashed" string, fabric, funny glasses |
10:55 | 11:05 | SESSION 1b THEORY |
Wave optics, Diffraction, and Resolution | BRITTA | "dashed" string |
11:05 | 11:15 | BREAK | COFFEE BREAK | ||
11:15 | 11:50 | SESSION 1a Practice 2 groups, 20min Rotation (17min at stations + 3min for switching in-between) Timer: CATARINA |
Interference and Diffraction | SEBASTIAN BRITTA RICCARDO |
Mach-Zehnder interferometer demo setup Ripple tank with various accessories |
11:50 | 12:40 | SESSION 1b Demo and Theory |
ABBE's diffraction demonstration | RUTH |
Dan's ABBE Diffraction demo setup |
12:40 | 13:45 | BREAK | LUNCH | ||
13:45 | 14:10 | 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 |
14:10 | 14:20 | SESSION 1c Theory |
Wrap - up & Q & A Diffraction |
JAN BioDIP TEAM |
|
14:20 | 14:40 | SESSION 2 Theory and Demo |
Lens aberrations and corrections finite versus infinite tube length objective labeling/reading |
JAN | lenses with various sizes and shapes |
14:40 | 14:45 | SESSION 3 Theory |
lateral vs angular magnification | BRITTA | |
14:45 | 14:55 | SESSION 2 Demo |
demo of spherical aberration | SEBASTIAN | magnetic lens + laser suitcase on white board |
14:55 | 15:10 | BREAK | COFFEE BREAK | ||
15:10 | 16:05 | SESSION 3 Practice 2 groups, 30min Rotation (25min at stations + 5min for switching in-between) Timer: CATARINA |
Cover glasses, sample mounting, Objective cleaning and infinity optics bench demo Objective reading |
JAN BRITTA |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, glass waste bin, cover glass thickness measure meter toilet paper and sand paper bench demo of infinity optics box with broken objectives + two 160 tube lens objectives cell culture microscope with finite tube length, red optics suitcase |
16:05 | 16:20 | SESSION 4 Theory |
Introduction to contrast | BRITTA | |
16:20 | 16:40 | 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 (within presentation) |
16:40 | 16:50 | BREAK | SHORT BREAK | ||
16:50 | 17:15 | SESSION 5b Practice |
Dark Field microscopy | BioDIP TEAM | diatom slides, pong water from CBG |
17:15 | 17:30 | SESSION 6a Theory |
Basics of Phase Contrast microscopy | SEBASTIAN | including videos from web and own |
17:30 | 17:35 | SESSION 6b Show & Tell |
show parts needed to Phase Contrast in condenser and respective objective | JAN | condenser with Phase annuli, phase contrast objective |
17:35 | 17:40 | SESSION 7 Demonstration |
Cheek cell prep, water from CBG pond | JAN | Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
17:40 | 18:10 | SESSION 6c Practice |
Phase Contrast microscopy | BioDIP TEAM | diatomes and similar samples cell culture microscope with cells in a dish as live example for phase contrast, water from CBG pond |
DAY THREE - Wed 29th June
organize pitchers with water and cups for short breaks
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:00 | Feedback & Recap discussion in groups | day 2 | BioDIP TEAM | Update question list, ask for feedback pair of sieves, torches, microscopes |
10:00 | 10:10 | BREAK | SHORT BREAK | BREAK | |
10:10 | 10:25 | SESSION 1 Demonstration |
Polarized light microscopy | JAN | for students and Sebastian: calcite crystal blocks, polarizers, paper with black spot; overhead projector stone samples, gummy bears, plastic dishes, duct tape, bones & cartilage (Jacqui’s lab) |
10:25 | 11:10 | SESSION 1 Theory and Demo |
Polarized light microscopy | SEBASTIAN JAN |
cell image library video info about LC-PolScope pol scope with rotatable stage |
11:10 | 11:20 | SESSION 1 Practice |
Polarized light microscopy | BioDIP TEAM | butterfly cuts, mouse skull slices from Tabler lab, hair, stone samples, benzocain crystals, tissue pieces ... |
11:20 | 11:40 | BREAK | COFFEE BREAK | BREAK | |
11:40 | 12:15 | SESSION 2 Theory and Demo |
Differential Interference Contrast (DIC) | BRITTA | DIC Nomarski |
12:15 | 13:00 | SESSION 2 Practice |
Differential Interference Contrast (DIC) | BioDIP TEAM JAN |
DIC-objectives with respective Nomarski prisms; cheek cell samples, diatoms |
13:00 | 13:45 | BREAK | LUNCH | ||
13:45 | 14:00 | Wrap-up compare methods |
Transmitted light contrasting techniques | BRITTA BioDIP TEAM |
first comparison than Quiz with various videos of the different techniques; Q & A |
14:00 | 14:25 | SESSION 3 Theory |
Fundamental concepts of fluorescence | BRITTA | fluorescent liquids in bottles plus lasers inside nice black box designed by Sebastian works nicely also in normally lit room |
14:25 | 15:05 | SESSION 4a Theory + Demo |
Introduction to fluorescence microscopes and light sources |
BRITTA | • Light sources • Lamp houses |
15:05 | 15:10 | SESSION Theory |
Introduction to laser safety | JAN (SEBASTIAN) |
|
15:10 | 15:25 | BREAK | COFFEE BREAK | BREAK | |
15:25 | 15:50 | SESSION 4b Theory |
Introduction to fluorescence microscopy Filters, spectra etc. |
CATARINA | Spectra Filters Filter cubes |
15:50 | 16:30 | SESSION 4c Practice |
Filters | BioDIP TEAM | laminated sheets with grids for spectra drawing red, green, blue, black board markers EtOH spray bottles, tissue |
16:30 | 16:35 | SESSION 4d Theory and Demo |
Introduction to fluorescence microscopy Filters, spectra objective transmission curves |
CATARINA | |
16:35 | 16:50 | SESSION 4e Theory and Demo |
Introduction to spectra viewer | SEBASTIAN | spectra viewer, searchlight from semrock |
16:50 | 16:55 | BREAK | SHORT BREAK | BREAK | |
16:55 | 17:05 | SESSION 4f Theory |
Epi illumination | JAN | |
17:05 | 18:00 | SESSION 4g Practice |
Spectraviewer Fluorescence imaging at microscopes |
SEBASTIAN BioDIP TEAM |
laminated sheets with DAPI/FITC/TRITC Spectra red, green, blue, board markers EtOH spray bottles + tissue Fluorescent labeled samples (Convalaria) |
DAY FOUR - Thu June 30th
organize pitchers with water and cups for short breaks
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | DEMO Activities | Materials needed |
9:00 | 10:00 | Feedback & Recap discussion in groups | day 3 | BioDIP TEAM | - | Update question list, ask for feedback |
10:00 | 10:05 | BREAK | SHORT BREAK | BREAK | BREAK | BREAK |
10:05 | 10:40 | SESSION 1 Theory |
Fluorophores | CATARINA | - | Molecular probes catalogue |
10:40 | 11:15 | SESSION 2a Demo |
Detectors | BRITTA JAN |
showing different chip sizes | CCD chip paper weight Demo: CCD chip under stereo microscope example cameras with differently sized chips |
11:15 | 11:25 | BREAK | SHORT BREAK | BREAK | BREAK | BREAK |
11:25 | 12:00 | SESSION 2a Demo |
Detectors | BRITTA JAN |
showing different chip sizes | CCD chip paper weight Demo: CCD chip under stereo microscope example cameras with differently sized chips |
12:00 | 12:10 | BREAK | SHORT BREAK | BREAK | BREAK | BREAK |
12:10 | 12:50 | SESSION 2b Theory |
Detectors | BRITTA | showing overflow with water and beakers | 3 different sized beakers + big one + one filled with water |
12:50 | 13:30 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
13:30 | 13:40 | SESSION 2c Demo |
Detectors | BRITTA | bench show | Axiocame on a stand with objectives PC nice sample for binning (tounge sample) |
13:40 | 13:55 | SESSION 2d Theory |
Detectors | BRITTA | advanced detectors lecture | |
13:55 | 14:00 | SESSION 2e Practice |
Detectors "QE" show |
JAN | students count times of laser pointer blinking | blinking laser pointer |
14:00 | 14:25 | SESSION 3a Theory |
Digital images | RICCARDO | Nyquist-Shannon what is a pixel spatial calibration |
comment about difference noise and background (unspecific) signal |
14:25 | 14:30 | SESSION 3a Demo |
Digital images | JAN | Nyquist-Shannon spatial calibration |
overhead projector sheets with different sized squares as example for dexel size gummi bears, Sesame seeds |
14:30 | 14:45 | 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) |
14:45 | 14:50 | SESSION 3a Practice |
calculating dexel/pixel size | RICCARDO | practice calculating needed dexel size for given optical setup | evaluation of the results from practical plus more calculation examples |
14:50 | 15:15 | SESSION 3b Theory |
Digital Imaging | RICCARDO | digitization in space, (time) & intensity aliasing |
- |
15:15 | 15:25 | BREAK | COFFEE BREAK | |||
15:25 | 16:25 | 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 / Convolaria ...) |
16:25 | 16:35 | SESSION 5a Theory |
OPTICAL SECTIONING introduction widefield & deconvolution |
JAN | - | labtop |
16:35 | 16:45 | SESSION 6 Theory |
CHROMATIC ABERRATION CORRECTION | JAN | ||
16:45 | 16:50 | BREAK | SHORT BREAK | |||
16:50 | 17:20 | SESSION 5b Theory & Demo |
OPTICAL SECTIONING Laser Scanning Confocal |
JAN | "confocal equipment": laser pointer, mirror, broken scanning mirror | |
17:20 | 17:50 | SESSION 5c Theory& Demo |
OPTICAL SECTIONING 2-Photon Microscopy |
SEBASTIAN JAN |
dual laser pointer (blue, green, red) piece of cheese to demonstrate penetration of diff. wavelength | |
17:50 | 18:15 | SESSION 5d Theory |
OPTICAL SECTIONING Spinning Disc Confocal |
BRITTA JAN |
beer bottle from Plzen | |
18:15 | 18:35 | SESSION 5d DEMO, voluntary 2 groups, 10min rotation (8min at stations + 2min for switching) timer: BRITTA |
OPTICAL SECTIONING Spinning Disc Confocal |
JAN BRITTA |
DAN's "spinning-disc-on-a-bench" |
DAY FIVE - Fri July 1st
organize pitchers with water and cups for short breaks
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:00 | Feedback & Recap discussion in groups | day 4 | BioDIP TEAM | Update Question list, ask for feedback |
10:00 | 10:10 | BREAK | BREAK | BREAK | |
10:10 | 10:25 | SESSION 1a Theory & Demo |
OPTICAL SECTIONING TIRF |
BRITTA | big plastic cuvette tank filled with FITC solution + red and green laser pointer |
10:25 | 10:45 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING Light sheet |
RICCARDO | glass block with brain/scull and red light sheet laser from ZEISS |
10:45 | 11:05 | SESSION 1c Demo |
OPTICAL SECTIONING Light sheet |
SEBASTIAN RICCARDO |
PETE's SPIM-in-a-suitcase |
11:05 | 11:10 | SESSION 1d Theory |
OPTICAL SECTIONING Apotome |
JAN | |
11:10 | 11:20 | SESSION 1e Theory |
OPTICAL SECTIONING final remarks |
JAN | |
11:20 | 11:35 | BREAK | BREAK | ||
11:35 | 12:10 | SESSION 2a Theory |
EXTENDED RESOLUTION SIM SMLM |
CATARINA | Laure's printed SIM patterns on paper and transparency for hands-on Moire pattern creation |
12:10 | 12:35 | SESSION 2b Theory |
EXTENDED RESOLUTION STED Airyscan/Pixel reassignment Sample Preparation |
BRITTA | |
12:35 | 12:45 | DISCUSSION | preparation for Monday hands-on sessions | SEBASTIAN BioDIP team |
white board |
12:45 | 13:30 | LUNCH | LUNCH | LUNCH | |
13:30 | 13:40 | SESSION Meet & Greet |
Meeting Alf Honigmann - Honigmann-lab (STED) | RICCARDO (JAN) |
Q & A with Alf STED, and cooperation possibilities |
13:40 | 13:50 | SESSION Meet & Greet |
Meeting Hella Hartmann, BioDIP Coordinator | HELLA (JAN) |
Q & A with HELLA about BioDIP and cooperation between the participating facilities BioDIP website |
13:50 | 14:00 | SESSION Meet & Greet |
Meeting Lena Hersemann, Leader Scientific Computing facility | LENA IVEY (JAN) |
introduction to bioinformatics service and image processing facility |
14:00 | 14:10 | SESSION Meet & Greet |
Meeting Sebastian Bundschuh, Leader Advanced Imaging Facility | SEBASTIAN (JAN) |
introduction to Advanced Imaging Facility |
14:10 | 14:20 | SESSION Meet & Greet |
Meeting Tobias Fürstenhaupt, Leader EM facility | TOBIAS (JAN) |
Q & A with Tobias about his facility and cooperation with LMF cut magnetic copper coil (Tobias) |
14:20 | 14:30 | SESSION 3 | Planning your Imaging Experiment | JAN (BRITTA) |
+ introduction to new form of questionnaire |
14:30 | 14:45 | SESSION 4 Theory & Discussion |
Controls in microscopy | BRITTA RICCARDO |
discussion about why controls are needed, what needs to be checked |
14:45 | 14:55 | BREAK | SHORT BREAK | BREAK | |
14:55 | 15:55 | SESSION 5 | Course evaluation | BioDIP TEAM | Gummy bear bags and/or fruits white board + marker |
DAY SIX - optional - Mon 4th July 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 / EXTENDED RESOLUTION | JAN BRITTA RICCARDO |
SD4, H2, H4; MZ1, LZ2, CZ6, CZ7, LV1 we need to decide which systems to use also block W7 and SD3 |
13:45 | 14:00 | Meeting students at switchboard |
OPTICAL SECTIONING / EXTENDED RESOLUTION | JAN BRITTA RICCARDO |
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 / EXTENDED RESOLUTION | JAN BRITTA RICCARDO |
SD4, H2, H4, W7 needs to be blocked as well; MZ; LZ2, LV1, SD3 needs to be blocked as well |
15:30 | 16:00 | BREAK | COFFEE | KATJA | |
16:00 | 17:30 | SESSION II hands-on |
OPTICAL SECTIONING / EXTENDED RESOLUTION | JAN BRITTA RICCARDO |
SD4, H2, H4, W7 needs to be blocked as well; MZ1; LZ2, LV1, SD3 needs to be blocked as well |
17:30 | 18:00 | ROUND-UP | FINAL GET TOGETHER | JAN BRITTA RICCARDO |
LMF office or atrium |