BasicCoursePhDProg - Basics in Light Microscopy - schedule April 2019

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PhD Program: Basics of Light Microscopy - LMF - Course April 2019

Tentative Schedule

SETUP - Wed March 27th and Thu March 28th (Fri March 29th TA course)

First time course teaching in CSBD SR top floor, also asked for usage of landing in front of it
Room is reserved from (incl) Wed, March 27th 2019 (full day) - Tues, April 9th, 8AM!
Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Wed
Setup of all needed course material in CSDB SR top floor Wed + Thurs, can already start Wed morning

Equipment needed

  • course handout for students
  • 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
  • Optical bench
  • Spinning disk gadget
  • Overhead projector with digital source switch
  • Polarizing sheets
  • Diffraction Grids
  • Sample map for each teaching station with: diatomes, liver tissue, Convolaria, tounge tissue (Laure is checking and updating maps)
  • microscope handout booklet for each teaching station
  • 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, 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 and tissue 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, (need to check carefully whether everything needed is there!)

DAY ONE - Mon 1st April

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 9:10 INTRODUCTION GENERAL OVERVIEW JAN
9:10 9:30 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 two - three volunteers)
9:30 09:50 Session 1a
Theory
PRINCIPLES OF LIGHT MICROSCOPY
Historical aspects
Very basic components and principles
(incl. refraction basics)
JAN
09:50 10:02 SESSION 1
Practice
students watch Airy pattern from hole in mirror BioDIP team mirror slides with hole on each teaching station
10:02 10:12 Session 1b
Theory
PRINCIPLES OF LIGHT MICROSCOPY
resolution basics
BRITTA
10:12 10:25 Session 1c
Theory
PRINCIPLES OF LIGHT MICROSCOPY
Historical aspects
Very basic components and principles
JAN
10:25 10:40 BREAK BREAK
10:40 11:23 SESSION 1
Practice
3 groups, 12min Rotation (+3min for switching stations)
Timer: SILKE
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
SEBASTIAN
*capillaries, oil
* water and oil tanks with glass rods from Anatol
* 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
11:23 12:03 SESSION 1d
Theory
Introduction to lenses and objectives
Magnification
JAN cut objective
12:03 12:05 SESSION 1e
Demonstration
Introduction to lenses and objectives
Numerical aperture
SEBASTIAN NOT:laminated sheet with cake image
instead: draw pizza on white/black board
12:05 13:00 LUNCH LUNCH
13:00 13:45 SESSION 1
Practice
15min (!) Rotation
Timer: SEBASTIAN
Milky Glass Block demo
Show and discuss microscope parts (upright and inverted)
NA measurements
JAN
BRITTA
LAURE
*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
13:45 14:25 SESSION 2
Theory
Microscope illumination
Conjugate planes
Apertures
JAN
14:25 14:43 BREAK BREAK
14:43 15:43 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
LAURE
JAN
*Peters microscope setup with artificial eye ball
*optical bench demonstrating a transmitted light microscope, incl. light source
conjugate planes scheme hand outs
15:43 16:00 SESSION 3
Theory
Koehler illumination
(Microscope alignment)
JAN
16:00 16:15 BREAK BREAK
16:15 17:15 SESSION 3a
Practice
Koehler illumination
(Microscope alignment)
BioDIP TEAM students manual microscopes, screwdrivers, nice brightfield sample
17:15 17:30 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"
17:30 17:45 SESSION 3b
Practice
finish Koehler illumination
(Microscope alignment)
BioDIP TEAM students manual microscopes, screwdrivers, nice brightfield sample
17:45 17:55 SESSION 3
Theory
Epi illumination JAN

DAY TWO - Tue 2nd April

organize pitchers with water and cups for short breaks

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
9:00 10:00 Recap day 1 BioDIP TEAM Questions
teaching microscopes; conjugate planes schemes
10:00 10:05 BREAK SHORT BREAK
10:05 10:10 Theory Introduction to
Peter Evennett's videos
Jan You tube videos
10:10 10:25 SESSION 1a
DEMONSTRATION
Diffraction and Diffraction slide fun
Diffraction string show
JAN diffraction slides, torch, "dashed" string, fabric, funny glasses
10:25 10:55 SESSION 1b
THEORY
Wave optics, Diffraction, and Resolution BRITTA "dashed" string
10:55 11:13 BREAK COFFEE BREAK
11:13 11:35 SESSION 1a
Practice Round
Group rotation
(10min each)
Timer: LAURE
Interference and Diffraction SEBASTIAN
BRITTA
Mach-Zehnder interferometer demo setup
Ripple tank with various accessories
11:35 11:55 SESSION 1b
Demo and Theory
ABBE's diffraction demonstration LAURE
(SILKE)
Dan's ABBE Diffraction demo setup
11:55 12:23 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
12:23 12:30 SESSION 1c
Theory
Wrap - up & Q & A
Diffraction
JAN
BioDIP TEAM
12:30 13:15 BREAK LUNCH
13:15 13:25 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')|
13:25 14:00 SESSION 2
Theory and Demo
Lens abERRations and corrections
finite versus infinite tube length
objective labeling/reading
JAN lenses with various sizes and shapes
14:00 14:10 SESSION 3
Theory
Objective reading
lateral vs angular magnification
JAN
BRITTA
objectives, eyepieces, overhead projector with digital source switch
14:10 14:15 SESSION 2
Demo
demo of spherical aberration SEBASTIAN magnetic lens + laser suitcase on white board
14:15 14:50 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, 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
14:50 15:00 BREAK COFFEE BREAK
15:00 15:35 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
15:35 15:50 SESSION 4
Theory
Introduction to contrast BRITTA
15:50 16:06 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
16:06 16:35 SESSION 5b
Practice
Dark Field microscopy BioDIP TEAM diatom slides
16:35 16:50 BREAK SHORT BREAK
16:50 17:12 SESSION 6a
Theory
Basics of Phase Contrast microscopy SEBASTIAN including videos from web and own
17:12 17:15 SESSION 6b
Show & Tell
show parts needed to Phase Contrast in condenser and respective objective JAN condenser with Phase annuli, phase contrast objective
17:15 17:20 SESSION 7
Demonstration
Cheek cell prep JAN Q-tips, slides, cover slips, PBS, plastic pipette, nail polish
17:20 18:00 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

DAY THREE - Wed 3rd April

organize pitchers with water and cups for short breaks

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
9:00 10:00 Recap day 2 BioDIP TEAM Questions, pair of sieves, torches, microscopes
10:00 10:07 BREAK SHORT BREAK BREAK
10:07 10:22 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, plastic rulers...
10:22 11:05 SESSION 1
Theory and Demo
Polarized light microscopy SEBASTIAN
JAN
cell image library video
info about LC-PolScope from openpolscope.org/
introduce responsible person for Brugues' PolScope
pol scope with rotatable stage
11:05 11:35 SESSION 1
Practice
Polarized light microscopy BioDIP TEAM hair, stone samples, benzocain crystals, tissue pieces ...
11:35 11:45 BREAK COFFEE BREAK BREAK
11:45 12:20 SESSION 2
Theory and Demo
Differential Interference Contrast (DIC) BRITTA DIC Nomarski
12:20 12:55 SESSION 2
Practice
Differential Interference Contrast (DIC) BioDIP TEAM
JAN
DIC-objectives with respective Nomarski prisms;
cheek cell samples, diatoms
12:55 13:00 SESSION
Meet & Greet
Meeting Mark Bickle, Leader Technology development studio
screening facility
MARK
(JAN)
Q & A with Mark about his facility
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; remind students on Friday's project discussion round
14:00 14:05 QUESTION ROUND Q & A about transmitted light contrasting techniques BRITTA
BioDIP TEAM
14:05 14:45 SESSION 3
Theory
Fundamental concepts of fluorescence BRITTA
SEBASTIAN
fluorescent liquids in bottles plus lasers inside nice black box designed by Sebastian
works nicely also in normally lit room
14:45 15:15 SESSION 4a
Theory + Demo
Introduction to fluorescence microscopes
and light sources
LAURE • Light sources
• Lamp houses
15:15 15:20 SESSION
Theory
Introduction to laser safety JAN
(SEBASTIAN)
15:20 15:40 BREAK COFFEE BREAK BREAK
15:40 15:55 SESSION 4b
Theory
Introduction to fluorescence microscopy
Filters, spectra etc.
LAURE
BRITTA
Spectra
Filters
Filter cubes
15:55 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
align="center" LAURE
BRITTA
16:35 16:50 SESSION 4e
Theory and Demo
Introduction to spectra viewer SEBASTIAN spectra viewer
16:50 16:55 BREAK SHORT BREAK BREAK
16:55 18:00 SESSION 4f
Practice
Spectraviewer
Aligment of Mercury arc lamps
Fluorescence imaging at microscopes
SEBASTIAN
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)
19:00 open end Dinner with all teachers BioDIP TEAM good mood, time

DAY FOUR - Thu 4th April

organize pitchers with water and cups for short breaks

FROM TO ACTIVITY TOPICS Responsible person(s) DEMO Activities Materials needed
9:00 10:00 Recap day 3 BioDIP TEAM - Questions (need to be adjusted to new course scheme!)
10:00 10:05 BREAK SHORT BREAK BREAK BREAK BREAK
10:05 10:25 SESSION 1
Theory
Fluorophores SEBASTIAN - did not do it this time - placeholder for next time
10:25 11:20 SESSION 2a
Theory
Detectors BRITTA - CCD chip paper weight
Demo: CCD chip under stereo microscope
example cameras showing different chip sizes
11:20 11:30 SESSION 2b
Demo
Detectors BRITTA bench show RT spot with RGB slider and camera objective
PC
nice sample for binning (coffee cup)
show grid at AC outlet in room
11:30 11:41 SESSION 2c
Theory
Detectors BRITTA advanced detectors lecture
11:41 11:45 SESSION 2d
Practice
Detectors
"QE" show
JAN students count times of laser pointer blinking blinking laser pointer
11:45 11:55 BREAK BREAK BREAK BREAK BREAK
11:55 12:17 SESSION 3a
Theory
Digital images LAURE Nyquist-Shannon
what is a pixel
spatial calibration
comment about difference noise and background (unspecific) signal
12:17 12:22 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
12:22 12:45 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)
12:45 12:52 SESSION 3a
Practice
calculating dexel/pixel size LAURE practice calculating needed dexel size for given optical setup evaluation of the results from practical plus more calculation examples
12:52 13:05 SESSION 3b
Theory
Quantitative Imaging LAURE digitization in space, (time) & intensity
aliasing
-
13:05 13:50 BREAK LUNCH LUNCH LUNCH LUNCH
13:50 15:15 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...)
15:15 15:30 BREAK COFFEE BREAK
15:30 15:40 SESSION
Meet & Greet
Meeting Isabel Raabe, BioDIP Coordinator ISA
(JAN)
Q & A with Isa about BioDIP and cooperation between the participating facilities BioDIP website
15:40 15:49 SESSION 5a
Theory
OPTICAL SECTIONING
introduction
widefield & deconvolution
JAN - labtop
15:49 16:00 SESSION 6
Theory
CHROMATIC ABERRATION JAN
16:00 16:18 SESSION 5b
Theory & Demo
OPTICAL SECTIONING
Laser Scanning Confocal
JAN "confocal equipment":
laser pointer, mirror, broken scanning mirror
16:18 16:43 BREAK BREAK
16:43 17:15 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
17:15 17:40 SESSION 5d
Theory
OPTICAL SECTIONING
Spinning Disc Confocal
BRITTA
JAN
beer bottle from Plzen
17:40 17:50 SESSION 5d
Demo
OPTICAL SECTIONING
Spinning Disc Confocal
JAN DAN's "spinning-disc-on-a-bench"

DAY FIVE - Fri 5th April

organize pitchers with water and cups for short breaks

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
9:00 10:05 Recap day 4 BioDIP TEAM Question sheets with the real case problem
calculators, pens
voting kit?
10:05 10:20 BREAK BREAK BREAK
10:20 10:36 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
10:36 10:55 SESSION 1b
Theory & Demo
OPTICAL SECTIONING
SPIM
SEBASTIAN glass block with brain/scull and red light sheet laser from ZEISS
10:55 11:07 SESSION 1c
Demo
OPTICAL SECTIONING
SPIM
SEBASTIAN PETE's SPIM-in-a-suitcase
11:07 11:15 SESSION 1d
Theory
OPTICAL SECTIONING
Apotome
JAN
11:15 11:30 SESSION 1e
Theory
OPTICAL SECTIONING
final remarks
JAN
11:30 11:45 BREAK BREAK
11:45 12:30 SESSION 2
Theory
EXTENDED RESOLUTION
SIM
STORM
STED
Airyscan
Sample Preparation
LAURE
12:30 12:32 DISCUSSION preparation for Monday hands-on sessions SEBASTIAN
BioDIP team
white board
12:32 13:18 LUNCH LUNCH LUNCH
13:18 13:23 SESSION
Meet & Greet
Meeting Riccardo Maraspini - Honigmann-lab (STED) RICCARDO
(JAN)
Q & A with Riccardo about Honigmann lab, STED, and cooperation possibilities
13:23 13:33 SESSION
Meet & Greet
Meeting Noreen Walker, Leader Scientific Computing facility NOREEN
(JAN)
introduction to bioinformatics service and image processing facility
13:33 13:40 SESSION 3 Planning your Imaging Experiment JAN
(LAURE)
+ introduction to new user project questions
13:40 13:55 SESSION 4a
Project discussion
One volunteer presents his/her imaging problem shortly and discuss it with the whole group BioDIP TEAM
+ NOREEN
NOTE: ask for volunteers already on Monday, than again on Wednesday
13:55 14:13 SESSION 4b
Project discussion
Second volunteer presents his/her imaging problem shortly and discuss it with the whole group BioDIP TEAM
+ NOREEN
NOTE: ask for volunteers already on Monday, than again on Wednesday
14:13 14:25 BREAK SHORT BREAK BREAK
14:25 14:55 SESSION 4c
Project discussion
Third volunteer presents his/her imaging problem shortly and discuss it with the whole group BioDIP TEAM
+ NOREEN
NOTE: ask for volunteers already on Monday, than again on Wednesday
14:45 14:55 SESSION
Meet & Greet
Meeting Nicola Maghelli, Leader Advanced Imaging Facility NICOLA
(JAN)
introduction to Advanced Imaging Facility
14:55 16:00 SESSION 5 Course evaluation BioDIP TEAM Gummy bear bags and/or fruits
white board + marker

DAY SIX - optional - Mon 8th 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 / EXTENDED RESOLUTION BioDIP team MZ1, LZ2, CZ6, SD4, H1, H2
we need to decide which systems to use
13:45 14:00 Meeting students
at switchboard
OPTICAL SECTIONING / EXTENDED 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 / EXTENDED RESOLUTION BioDIP team MZ1, LZ2, CZ6, SD4, H1, H2
15:30 16:00 BREAK COFFEE KATJA
16:00 17:30 SESSION II
hands-on
OPTICAL SECTIONING / EXTENDED RESOLUTION BioDIP TEAM MZ1, LZ2, CZ6, SD4, H1, H2
17:30 18:00 ROUND-UP FINAL GET TOGETHER BioDIP TEAM LMF office or atrium

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