BasicsCoursePhDprog-PeterEvennett - schedule Oct. 2013
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Revision as of 18:27, 23 October 2013
Contents |
PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course October 2013
SETUP - Fri 11th Oct
Setup of all needed course material in Galeria
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 (14th Oct)
| 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, calc refraction |
JAN BRITTA |
*capillaries, oil * coin-in-cup, water * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and milky water |
| 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 (15th Oct)
| 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 |
| 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 (16th Oct)
| 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 and Objective cleaning Objective reading |
JAN BRITTA |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter 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 | cheek cell samples, diatoms | |
| 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 |
BRITTA JAN |
• Light sources • Lamp houses | |
| 19:30 | open end | Dinner | with Peter | BioDIP TEAM |
DAY FOUR (17th Oct)
| 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 | BRITTA 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 | 11:15 | BREAK | BREAK | BREAK | BREAK | BREAK |
| 11:00 | 12:00 | SESSION 1 Practice |
Fluorescence imaging at microscopes | LMF TEAM | - | • Fluorescent labeled samples (Convallaria) |
| 12:00 | 13:00 | SESSION 2 Theory & Practice |
Detectors | BRITTA | • CCD chip • example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope |
|
| 13:00 | 14:00 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
| 14:00 | 14:30 | SESSION 2 Practice |
Basic camera "vocabulary" on students microscopes | LMF TEAM | - | checklist |
| 14:30 | 15:45 | SESSION 3 Theory |
What is a pixel Analog to Digital conversion Nuyquist-Shannon Quantitative Imaging Spatial Calibration |
BERT | - | • pixel size calculation on a given optical setup |
| 15:45 | 16:00 | BREAK | BREAK | |||
| 16:00 | 16:45 | SESSION 4a Practice |
camera discussion on student microscopes | LMF TEAM | • guidelines for choosing camera • spatial calibration • camera specs sheet discussion |
• camera specs sheets • checklist |
| 16:45 | 18:00 | SESSION 4b 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 |
DAY FIVE (18th Oct)
| 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 |
