BasicsCoursePhDprog-PeterEvennetApril2013
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| − | | 11:00|| | + | | 11:00||11:30||align="center"|Session 2a <br> DEMONSTRATION || align="center"|Diffraction and Diffraction slide fun <br> Diffraction string show||align="center"|PETER EVENNETT || align="center" | Diffraction slides, torch, "dashed" string |
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| + | |style="background:Salmon;"| 11:30 | ||
| + | |style="background:Salmon;"|12:45||align="center" style="background:Salmon;"|Special: <br> MPI Technology Day (large auditorium)||align="center" style="background:Salmon;"| talks from GE Healthcare <br> Nikon <br> Zeiss ||align="center" style="background:Salmon;"|Dan White <br> Niklas Senghaas <br> Olaf Selchow|| align="center" style="background:Salmon;"| | ||
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|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | |align="center" style="background:mediumseagreen;"|'''LUNCH'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | ||
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| − | | 13: | + | | 13:30||14:30||align="center"| SESSION 2b <br> Demo and Theory || align="center"| Peter's Diffraction setup LIVE <br> or <br> Dan's diffraction setup demonstration ||align="center" |PETER <br> or <br> SILKE ||align="center" |Dan's ABBE Diffraction demo setup |
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| − | | 14: | + | | 14:30||15:15||align="center"|SESSION 3<br>Theory and Demo||align="center" | Lens aberrations and corrections ||align="center" |PETER EVENNETT <br> JAN|| align="center" |magnetic lens + laser suitcase on white board| |
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| − | | 15: | + | | 15:15||15:45||align="center"|SESSION 4<br>Theory||align="center" | Introduction to contrast ||align="center" |PETER EVENNETT || |
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| style="background:mediumseagreen;"|'''15:45''' | | style="background:mediumseagreen;"|'''15:45''' | ||
| + | | style="background:mediumseagreen;"|'''16:00''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | |align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | ||
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| − | | | + | | 16:00 || 16:20 ||align="center"|SESSION 4a<br>Theory|| align="center"| Dark Field microscopy||align="center" |PETER EVENNETT || |
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| − | |style="background:LemonChiffon;"| 16: | + | |style="background:LemonChiffon;"| 16:20 |
| − | |style="background:LemonChiffon;"| 16: | + | |style="background:LemonChiffon;"| 16:45 ||align="center" style="background:LemonChiffon;"|SESSION 4a<br>Practice|| align="center" style="background:LemonChiffon;"|Dark Field microscopy||align="center" style="background:LemonChiffon;"|LMF TEAM || align="center" style="background:LemonChiffon;"| diatome slides |
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| − | | 16: | + | | 16:45||17:05||align="center"|SESSION 4b<br>Theory|| align="center"|Basics of Phase Contrast microscopy ||align="center" |PETER EVENNETT || |
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| − | |style="background:LemonChiffon;"| | + | |style="background:LemonChiffon;"| 17:05 |
| − | |style="background:LemonChiffon;"|17: | + | |style="background:LemonChiffon;"|17:45||align="center" style="background:LemonChiffon;"|SESSION 4b<br>Practice|| align="center" style="background:LemonChiffon;"|Phase Contrast microscopy ||align="center" style="background:LemonChiffon;"|LMF TEAM || align="center" style="background:LemonChiffon;"| cheek cell samples |
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| 16:15||17:50||align="center"|SESSION 3<br>Theory & Practice|| align="center"|Detectors ||align="center" |BRITTA||align="center" | • CCD chip <br> • example cameras showing different chip sizes <br> • RGB Slider Spot Camera setup <br> Demo: CCD chip under stereo microscope | | 16:15||17:50||align="center"|SESSION 3<br>Theory & Practice|| align="center"|Detectors ||align="center" |BRITTA||align="center" | • CCD chip <br> • example cameras showing different chip sizes <br> • RGB Slider Spot Camera setup <br> Demo: CCD chip under stereo microscope | ||
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| align="center" style="background:#f0f0f0;"|'''Materials needed''' | | align="center" style="background:#f0f0f0;"|'''Materials needed''' | ||
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| − | | 9:00||10:00||align="center"|Recap ||align="center" | day 3 ||align="center" |LMF TEAM |||| | + | | 9:00||10:00||align="center"|Recap (Demo) ||align="center" | day 3 ||align="center" |LMF TEAM (JAN) ||align="center" |PIXELS ||align="center" |Sesame seeds, sunflower seeds, nudels, gumibears and a checker board (on Polylux) |
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| − | | 10:00||10:45||align="center"|SESSION 1<br>Theory||align="center" | Fundamental concepts of fluorescence ||align="center" |JAN||align="center" |- ||align="center" | | + | | 10:00||10:45||align="center"|SESSION 1<br>Theory||align="center" | Fundamental concepts of fluorescence ||align="center" |JAN||align="center" |- ||align="center" |fluorescent liquids in bottles plus laser pointer (blue, green, red) |
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| style="background:mediumseagreen;"|'''14:00''' | | style="background:mediumseagreen;"|'''14:00''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH''' | |align="center" style="background:mediumseagreen;"|'''LUNCH''' | ||
| − | |align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''|| style="background:mediumseagreen;"|Optional: LMF tour | + | |align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" style="background:mediumseagreen;"|Optional: LMF tour |
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| − | | 14:00|| | + | | 14:00||14:10||align="center"|SESSION 2|| align="center"|Planning your Imaging Experiment ||align="center" |DAVIDE||align="center" | |
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| − | | | + | | 14:10||15:15||align="center"|SESSION 3<br> Project discussion|| align="center"|Selected (volunteering) users present their imaging problems shortly and discuss it with the whole group ||align="center" |LMF TEAM||align="center" |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 |
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| 15:15||16:00||align="center"|SESSION 3|| align="center"|Course evaluation ||align="center" |LMF TEAM||align="center" | | | 15:15||16:00||align="center"|SESSION 3|| align="center"|Course evaluation ||align="center" |LMF TEAM||align="center" | | ||
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Latest revision as of 16:00, 8 March 2013
Contents |
[edit] PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course April 2013
[edit] Setup -Fri 05 April
Setup of all needed course material in Small Auditorium
Equipment needed
- Microscopes
- Optical bench
- Spinning disk gadget
- Polarazing sheets
- Diffraction Grids
- Fluorescent samples
- Fluorescent Beads (Prepare slides)
- First day Handout for students
- Light torches
- cameras and monitors
- Cleaning stations for each table
- condenser screwdrivers for each microsocpe
- oil/DIC objectives for each microscope (next to stand)
- 2 polarization filters for each microscope
[edit] DAY ONE (8th April)
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 09:30 | FINAL PREP | Test everything works | LMF | |
| 9:40 | 10:25 | INTRODUCTION | COURSE INTRO WHO is WHO? Round table |
LMF TEAM | White board and pen |
| 10:25 | 11:05 | Session 1 Theory |
PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles ( incl. Refraction-basics) |
PETER EVENNETT (JAN) | Jan shortly showing airy pattern from hole in mirror at one of the teaching microsopes (+ screen) |
| 11:05 | 11:15 | BREAK | BREAK | ||
| 11:15 | 11:50 | SESSION 1 Practice SHORT (5min !!!) Rotation |
capillary/plastic (Huisken) in oil demo Coin-in-cup demo red and green laser through milky water with black background |
(PETE)Jan PETER BRITTA (SILKE) |
*capillaries, oil * coin-in-cup, water *laser pointer, glass with "milky" water and black background |
| 11:50 | 12:45 | 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 |
| 12:45 | 13:45 | 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 SILKE |
*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 |
[edit] DAY TWO (9th April)
| 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 | 12:45 | Special: MPI Technology Day (large auditorium) |
talks from GE Healthcare Nikon Zeiss |
Dan White Niklas Senghaas Olaf Selchow |
|
| 12:45 | 13:30 | BREAK | LUNCH | ||
| 13:30 | 14:30 | SESSION 2b Demo and Theory |
Peter's Diffraction setup LIVE or Dan's diffraction setup demonstration |
PETER or SILKE |
Dan's ABBE Diffraction demo setup |
| 14:30 | 15:15 | SESSION 3 Theory and Demo |
Lens aberrations and corrections | PETER EVENNETT JAN |
magnetic lens + laser suitcase on white board| |
| 15:15 | 15:45 | SESSION 4 Theory |
Introduction to contrast | PETER EVENNETT | |
| 15:45 | 16:00 | BREAK | COFFEE BREAK | ||
| 16:00 | 16:20 | SESSION 4a Theory |
Dark Field microscopy | PETER EVENNETT | |
| 16:20 | 16:45 | SESSION 4a Practice |
Dark Field microscopy | LMF TEAM | diatome slides |
| 16:45 | 17:05 | SESSION 4b Theory |
Basics of Phase Contrast microscopy | PETER EVENNETT | |
| 17:05 | 17:45 | SESSION 4b Practice |
Phase Contrast microscopy | LMF TEAM | cheek cell samples |
[edit] DAY THREE (10th April)
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 10:00 | Recap | day 2 | LMF TEAM | Questions |
| 10:00 | 10:30 | SESSION 1 Theory |
Objective reading | PETER EVENNETT LMF TEAM |
objectives, eyepieces, polylux |
| 10:30 | 10:45 | BREAK | BREAK | BREAK | |
| 10:45 | 11:45 | SESSION 1 Practice Group rotation |
Cover glasses, sample mounting and Objective cleaning Objective reading |
JAN BRITTA, SILKE |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter at least 7 different, "interesting" objectives (for a group of 6-7) |
| 12:15 | 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 | 17:50 | SESSION 3 Theory & Practice |
Detectors | BRITTA | • CCD chip • example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope |
[edit] DAY FOUR (11th April)
| 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 |
Fundamental concepts of fluorescence | JAN | - | fluorescent liquids in bottles plus laser pointer (blue, green, red) |
| 10:45 | 11:00 | BREAK | BREAK | BREAK | BREAK | BREAK |
| 11:00 | 12:15 | SESSION 2 Theory & Practice |
Fluorescence Microscopy | DAVIDE | • Light sources • Lamp houses • Spectra • Filters • Filter cubes • Filter spectral charts of each microscope (laminated) |
• Spare lamp houses • Lamps • Ocean optics equipment • Four (4) different Filter-sets (cubes), with the appropriate descriptions • diagramms for drawing filter/fluorophore spectra |
| 12:15 | 13:00 | SESSION 2 Practice |
Fluorescence imaging at microscopes | LMF TEAM | - | • Fluorescent labeled samples (Convallaria) |
| 13:00 | 14:00 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
| 14:00 | 15:45 | SESSION 3 Theory & Practice |
What is a pixel Analog to Digital conversion Nuyquist-Shannon Quantitative Imaging Spatial Calibration |
BERT DAVIDE |
- | • pixel size calculation on a given optical setup |
| 15:45 | 16:00 | BREAK | BREAK | |||
| 16:00 | 18:00 | SESSION 4 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 |
[edit] DAY FIVE (12th April)
| 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 |
