BasicsCoursePhDprog-PeterEvennett - schedule Oct. 2013
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− | | 15:05||15:25||align="center"|SESSION 3b<br>Theory|| align="center"|Quantitative Imaging | + | | 15:05||15:25||align="center"|SESSION 3b<br>Theory|| align="center"|Quantitative Imaging ||align="center" |BERT||align="center" |digitization in space, time & intensity<br>aliasing ||align="center" |- |
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− | |style="background:LemonChiffon;"|16: | + | |style="background:LemonChiffon;"|16:55|| align="center" style="background:LemonChiffon;"|SESSION 4a+b<br>Practice|| align="center" style="background:LemonChiffon;"|camera discussion on student microscopes|| align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"|check out basic camera vocabulary<br> discussing spec sheets of student microscope cameras<br>spatial calibration with ruler and FIJI|| align="center" style="background:LemonChiffon;"|camera spec sheets<br>Hamamatsu camera comparison list <br>camera vocabulary checklist <br> microscope ruler |
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− | |style="background:LemonChiffon;"|16: | + | |style="background:LemonChiffon;"|16:55 |
− | |style="background:LemonChiffon;"|18: | + | |style="background:LemonChiffon;"|18:00ish<br>open end|| align="center" style="background:LemonChiffon;"|SESSION 4c<br>Practice|| align="center" style="background:LemonChiffon;"|Imaging with CCD cameras using LMF systems|| align="center" style="background:LemonChiffon;"|JAN<br>BRITTA<br>BERT|| align="center" style="background:LemonChiffon;"|camera spec sheet of respective cameras<br>LUT, saturation, histogram etc<br>BioDIP Wiki|| align="center" style="background:LemonChiffon;"|Microscopes: <br> N-Storm (BRITTA, 4 students)<br> W1 Oly-TIRF (BERT, 3 students) <br> self-built-system (JAN, 4 students)) <br>Fluorescence Sample slides (Kidney / Cells...)<br> camera spec sheets of respective camera |
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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: | + | | 9:00||10:00||align="center"|Recap ||align="center" | day 4 ||align="center" |BioDIP TEAM||align="center"|Question sheets<br>calculators, pens |
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+ | |- | ||
+ | | 10:00||10:30||align="center"|SESSION 1a<br>Theory ||align="center" | OPTICAL SECTIONING<br>introduction<br>widefield & deconvolution<br>chromatic aberration & correction ||align="center" |JAN||align="center"|labtop | ||
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| style="background:mediumseagreen;"|'''10:45''' | | style="background:mediumseagreen;"|'''10:45''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
− | |align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"| | + | |align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"| |
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− | |10:45|| | + | |10:45||11:30||align="center"|SESSION 1b<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Laser Scanning Confocal<br>2PM ||align="center" |JAN<br>BRITTA ||align="center" |"confocal equipment": <br> laser pointer, mirror, broken scanning mirror <br> dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength |
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− | | style="background:mediumseagreen;"|''' | + | |11:30||12:15||align="center"|SESSION 1c<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Spinning disc confocal<br>TIRF<br>SPIM ||align="center" |BRITTA<br>JAN ||align="center" |DAN's "spinning-disc-on-a-bench"<br>small glass cube with olive oil over milky water plus<br>5mW blue laser pointer (CRTD)<br>glass block with brain/scull and red light sheet laser from ZEISS |
− | | style="background:mediumseagreen;"|''' | + | |- |
+ | |- | ||
+ | |12:15||12:30||align="center"|SESSION 1c<br>Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |PETE ||align="center" |PETE's SPIM-in-a-suitcase (on a bench this time)<br>glass block with whole scull<br>PETE's light sheet laser from whicked laser | ||
+ | |- | ||
+ | |- | ||
+ | |12:30||12:40||align="center"|SESSION 1d<br>Theory||align="center" | OPTICAL SECTIONING<br>Apotome<br>final remarks ||align="center" |JAN ||align="center" | | ||
+ | |- | ||
+ | |- | ||
+ | | style="background:mediumseagreen;"|'''12:40''' | ||
+ | | style="background:mediumseagreen;"|'''13:45''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH''' | |align="center" style="background:mediumseagreen;"|'''LUNCH''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" 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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− | | | + | | 13:45||14:00||align="center"|SESSION 2|| align="center"|Planning your Imaging Experiment ||align="center" |BERT||align="center" | + introduction to new user project questions |
+ | |- | ||
+ | |- | ||
+ | | 14:00||14:50||align="center"|SESSION 3<br> Project discussion|| align="center"|Three volunteer users present their imaging problems shortly and discuss it with the whole group ||align="center" |BioDIP TEAM||align="center" |NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low | ||
+ | |- | ||
|- | |- | ||
+ | | 14:50||15:50||align="center"|SESSION 3|| align="center"|Course evaluation ||align="center" |BioDIP TEAM||align="center" |Gummy bear bags (last time it was apples :-))<br>white board + marker | ||
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− | |||
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+ | | 15:50||16:00||align="center"|SESSION 4|| align="center"|Introduction to BioDIP Wiki ||align="center" |BRITTA||align="center" | lab top | ||
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|} | |} |
Latest revision as of 18:17, 4 November 2013
Contents |
[edit] PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course October 2013
[edit] 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
[edit] 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" |
[edit] 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 |
[edit] 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 |
[edit] 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 | 11:20 | BREAK | BREAK | BREAK | BREAK | BREAK |
11:20 | 12:15 | SESSION 1 Practice |
Fluorescence imaging at microscopes | BioDIP TEAM | - | laminated sheets with DAPI/FITC/TRITC Spectra red, green, blue, board markers EtOH spray bottles + tissue Fluorescent labeled samples (Convallaria) |
12:15 | 12:55 | SESSION 2 Theory |
Detectors | BRITTA | - | CCD chip paper weight example cameras showing different chip sizes • RGB Slider Spot Camera setup Demo: CCD chip under stereo microscope (for later) |
12:55 | 13:50 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
13:50 | 14:20 | SESSION 2 Demo & Theory |
Detectors | BRITTA | bench show advacned detectors lecture |
RT spot with slider and camera objective PC nice sample for binning |
14:20 | 14:25 | SESSION 2 Practice |
Detectors "QE" show |
JAN | students count times of laser pointer blinking | blinking laser pointer |
14:25 | 14:50 | SESSION 3a Theory |
Digital sampling | BERT | Nyquist-Shannon what is a pixel spatial calibration |
- |
14:50 | 15:05 | SESSION 3 Practice |
calculating dexel/pixel size | BioDIP TEAM | practice calculating needed dexel size for given optical setup | calculator text with given optical setup |
15:05 | 15:25 | SESSION 3b Theory |
Quantitative Imaging | BERT | digitization in space, time & intensity aliasing |
- |
15:25 | 15:45 | BREAK | BREAK | |||
15:45 | 16:55 | SESSION 4a+b Practice |
camera discussion on student microscopes | BioDIP TEAM | check out basic camera vocabulary discussing spec sheets of student microscope cameras spatial calibration with ruler and FIJI |
camera spec sheets Hamamatsu camera comparison list camera vocabulary checklist microscope ruler |
16:55 | 18:00ish open end |
SESSION 4c Practice |
Imaging with CCD cameras using LMF systems | JAN BRITTA BERT |
camera spec sheet of respective cameras LUT, saturation, histogram etc BioDIP Wiki |
Microscopes: N-Storm (BRITTA, 4 students) W1 Oly-TIRF (BERT, 3 students) self-built-system (JAN, 4 students)) Fluorescence Sample slides (Kidney / Cells...) camera spec sheets of respective camera |
[edit] DAY FIVE (18th Oct)
FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
9:00 | 10:00 | Recap | day 4 | BioDIP TEAM | Question sheets calculators, pens |
10:00 | 10:30 | SESSION 1a Theory |
OPTICAL SECTIONING introduction widefield & deconvolution chromatic aberration & correction |
JAN | labtop |
10:30 | 10:45 | BREAK | BREAK | BREAK | |
10:45 | 11:30 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING Laser Scanning Confocal 2PM |
JAN BRITTA |
"confocal equipment": laser pointer, mirror, broken scanning mirror dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength |
11:30 | 12:15 | SESSION 1c Theory & Demo |
OPTICAL SECTIONING Spinning disc confocal TIRF SPIM |
BRITTA JAN |
DAN's "spinning-disc-on-a-bench" small glass cube with olive oil over milky water plus 5mW blue laser pointer (CRTD) glass block with brain/scull and red light sheet laser from ZEISS |
12:15 | 12:30 | SESSION 1c Demo |
OPTICAL SECTIONING SPIM |
PETE | PETE's SPIM-in-a-suitcase (on a bench this time) glass block with whole scull PETE's light sheet laser from whicked laser |
12:30 | 12:40 | SESSION 1d Theory |
OPTICAL SECTIONING Apotome final remarks |
JAN | |
12:40 | 13:45 | LUNCH | LUNCH | LUNCH | Optional: LMF tour |
13:45 | 14:00 | SESSION 2 | Planning your Imaging Experiment | BERT | + introduction to new user project questions |
14:00 | 14:50 | SESSION 3 Project discussion |
Three volunteer users present their imaging problems shortly and discuss it with the whole group | BioDIP TEAM | NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low |
14:50 | 15:50 | SESSION 3 | Course evaluation | BioDIP TEAM | Gummy bear bags (last time it was apples :-)) white board + marker |
15:50 | 16:00 | SESSION 4 | Introduction to BioDIP Wiki | BRITTA | lab top |