BasicCoursePhDProg - Basics in Light Microscopy - schedule March 2020
From BioDIP
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(copied schedule content from April 2019, adjusted first dates at the top) |
(→DAY FOUR - Thu March 26th) |
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| − | ==PhD Program: Basics of Light Microscopy - LMF - Course | + | ==PhD Program: Basics of Light Microscopy - LMF - Course March 2020 == |
===Tentative Schedule=== | ===Tentative Schedule=== | ||
| Line 5: | Line 5: | ||
=== SETUP - Thu March 19th and Fri March 20th=== | === SETUP - Thu March 19th and Fri March 20th=== | ||
Again in CSBD SR top floor, also using landing in front of it | Again in CSBD SR top floor, also using landing in front of it | ||
| − | <br>Room is reserved from (incl) Thu, March 19th 2020 | + | <br>Room is reserved from (incl) Thu, March 19th 2020 4:00PM - Tues, March 31st, 5PM! |
<br> Mon March 30th and Tue March 31st is basically to have room blocked for Building maintenance to put back all tables and chairs | <br> Mon March 30th and Tue March 31st is basically to have room blocked for Building maintenance to put back all tables and chairs | ||
<br>Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Wed | <br>Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Wed | ||
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* Box with red, green, blue, black board marker, pen, pencil, sharpener, ruler, calculator for each microscope, <span style="color:red; ">(need to check carefully whether everything needed is there!) | * Box with red, green, blue, black board marker, pen, pencil, sharpener, ruler, calculator for each microscope, <span style="color:red; ">(need to check carefully whether everything needed is there!) | ||
| − | === DAY ONE - Mon | + | === DAY ONE - Mon 23rd March === |
organize pitchers with water and cups for the short breaks | organize pitchers with water and cups for the short breaks | ||
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| − | | 9: | + | | 9:00||9:05||align="center"|INTRODUCTION||align="center" | GENERAL OVERVIEW ||align="center" |JAN || align="center"| |
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| − | | 9: | + | | 9:05||9:25||align="center"|INTRODUCTION||align="center" | COURSE INTRO <br> WHO is WHO? Round table||align="center" |BioDIP TEAM || align="center"| White board and pen; ask students for volunteering for Friday's project discussion round<br>(we need two - three volunteers) |
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| − | | 9: | + | | 9:25||09:45||align="center"|Session 1a<br>Theory||align="center" | PRINCIPLES OF LIGHT MICROSCOPY<br>Historical aspects<br>Very basic components and principles <br>(incl. refraction basics)||align="center" |JAN ||align="center"| |
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| − | | style="background:LemonChiffon;"| 09: | + | | style="background:LemonChiffon;"| 09:45|| style="background:LemonChiffon;"| 09:55 |
|align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice|| align="center" style="background:LemonChiffon;"|students watch Airy pattern from hole in mirror||align="center" style="background:LemonChiffon;"|BioDIP team || align="center" style="background:LemonChiffon;" |mirror slides with hole on each teaching station | |align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice|| align="center" style="background:LemonChiffon;"|students watch Airy pattern from hole in mirror||align="center" style="background:LemonChiffon;"|BioDIP team || align="center" style="background:LemonChiffon;" |mirror slides with hole on each teaching station | ||
|- | |- | ||
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| − | | | + | | 09:55||10:05||align="center"|Session 1b<br>Theory||align="center" | PRINCIPLES OF LIGHT MICROSCOPY<br>resolution basics||align="center" |BRITTA||align="center"| |
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| − | | 10: | + | | 10:05||10:20||align="center"|Session 1c<br>Theory||align="center" | PRINCIPLES OF LIGHT MICROSCOPY<br>Historical aspects<br>Very basic components and principles ||align="center" |JAN ||align="center"| |
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| − | | style="background:mediumseagreen;"|'''10: | + | | style="background:mediumseagreen;"|'''10:20''' |
| − | | style="background:mediumseagreen;"|'''10: | + | | style="background:mediumseagreen;"|'''10:35''' |
|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;"| | |align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"| ||align="center" style="background:mediumseagreen;"| | ||
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| − | | style="background:LemonChiffon;"| 10: | + | | style="background:LemonChiffon;"| 10:35|| style="background:LemonChiffon;"| 11:20 |
| − | |align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice<br> 3 groups, | + | |align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice<br> 3 groups, 15min Rotation <br>(12min at stations + 3min for switching in-between)<br>Timer: SILKE|| align="center" style="background:LemonChiffon;"|capillary/plastic (Huisken) in oil demo <br>Coin-in-cup demo<br>red, green laser through water bath -<br> measure angles, calculate refraction; <br>show immersion objectives<br> measure refraction with modern refractometer||align="center" style="background:LemonChiffon;"|JAN <br>BRITTA<br>SEBASTIAN || align="center" style="background:LemonChiffon;" |*capillaries, oil <br>* water and oil tanks with glass rods from Anatol <br>* coin-in-cup, water, beaker for water <br>* red/green laser pointer with holder stand, plastic refraction demo setup with protractor and water, laminated image of ice bear in water/air <br> *water, glycerol, oil immersion objectives (take from Tuesday box!)<br>*refractometer |
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| − | | 11: | + | | 11:20||12:00||align="center"|SESSION 1d <br>Theory|| align="center" | Introduction to lenses and objectives <br>Magnification<br>||align="center" |JAN || align="center" | cut objective <br> foam objective |
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| − | | 12: | + | | 12:00||12:05||align="center"|SESSION 1e <br>Demonstration|| align="center" | Introduction to lenses and objectives<br>Numerical aperture||align="center" |SEBASTIAN || align="center" | NOT:laminated sheet with cake image<br> instead: draw pizza on white/black board (pizza or cake) |
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| − | | style="background:mediumseagreen;"|'''12: | + | | style="background:mediumseagreen;"|'''12:05''' |
| style="background:mediumseagreen;"|'''13:00''' | | style="background:mediumseagreen;"|'''13:00''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH''' | |align="center" style="background:mediumseagreen;"|'''LUNCH''' | ||
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| − | | style="background:LemonChiffon;"| 13:00|| style="background:LemonChiffon;"| 13: | + | | style="background:LemonChiffon;"| 13:00|| style="background:LemonChiffon;"| 13:45 |
| − | |align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice<br> 15min ( | + | |align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice<br> 3 groups, 15min Rotation <br>(12min at stations + 3min for switching in-between) <br>Timer: SEBASTIAN <br>SILKE|| align="center" style="background:LemonChiffon;"|Milky Glass Block demo <br>Show and discuss microscope parts (upright and inverted)<br>NA measurements||align="center" style="background:LemonChiffon;"|JAN<br>BRITTA<br>LAURE || align="center" style="background:LemonChiffon;" |*milky glass block, teaching microscope, coloured filters for microscope, iris objective <br> *slides with arrows, simple upright and inverted microscope <br> *horizontal protractor on stand, objective holder, 2 air objective with different (!) NAs (and maybe an iris objective), calculator, pencils, rubber |
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| − | |13: | + | |13:45|| 14:25||align="center"|SESSION 2<br>Theory||align="center"| Microscope illumination <br> Conjugate planes<br> Apertures||align="center" |MICHAEL ZOELFFEL<br>JAN || |
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| − | | style="background:mediumseagreen;"|'''14: | + | | style="background:mediumseagreen;"|'''14:25''' |
| style="background:mediumseagreen;"|'''14:45''' | | style="background:mediumseagreen;"|'''14:45''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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|style="background:LemonChiffon;"|14:45 | |style="background:LemonChiffon;"|14:45 | ||
| − | |style="background:LemonChiffon;"|15:45 || align="center" style="background:LemonChiffon;"|SESSION 2<br>Practice<br> | + | |style="background:LemonChiffon;"|15:45 || align="center" style="background:LemonChiffon;"|SESSION 2<br>Practice<br> 2 groups, 30min Rotation <br>(27min at stations + 3min for switching in-between)<br>Timer: SEBASTIAN<br>SILKE|| align="center" style="background:LemonChiffon;"|conjugate planes on Peters microscope <br> conjugate planes on optical bench +<br>effect of changing field and aperture diaphragms on demo scope||align="center" style="background:LemonChiffon;"|LAURE<br>JAN ||align="center" style="background:LemonChiffon;"| *Peters microscope setup with artificial eye ball <br> *optical bench demonstrating a transmitted light microscope, incl. light source<br>conjugate planes scheme hand outs |
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| − | |15:45||16: | + | |15:45||16:00||align="center"|SESSION 3<br>Theory||align="center" |Koehler illumination <br> (Microscope alignment)||align="center" |MICHAEL ZOELFFEL<br>JAN || |
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| − | | style="background:mediumseagreen;"|'''16: | + | | style="background:mediumseagreen;"|'''16:00''' |
| style="background:mediumseagreen;"|'''16:20''' | | style="background:mediumseagreen;"|'''16:20''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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|style="background:LemonChiffon;"|16:20 | |style="background:LemonChiffon;"|16:20 | ||
| − | |style="background:LemonChiffon;"|17: | + | |style="background:LemonChiffon;"|17:20||align="center" style="background:LemonChiffon;"|SESSION 3a<br>Practice|| align="center" style="background:LemonChiffon;"|Koehler illumination<br>(Microscope alignment)||align="center" style="background:LemonChiffon;"|BioDIP TEAM ||align="center" style="background:LemonChiffon;"|students manual microscopes, screwdrivers, nice brightfield sample |
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| − | |style="background:LemonChiffon;"|17: | + | |style="background:LemonChiffon;"|17:20 |
|style="background:LemonChiffon;"|17:30||align="center" style="background:LemonChiffon;"|SESSION 4<br>Theory & Practice|| align="center" style="background:LemonChiffon;"|Eyepieces<br>Depth of field<br> Depth of focus<br>more Koehler||align="center" style="background:LemonChiffon;"|BRITTA<br>BioDIP TEAM ||align="center" style="background:LemonChiffon;"|students microscopes with 10x/0.25 and 40x/0.65 objectives<br>Stereoscope with a "sample" | |style="background:LemonChiffon;"|17:30||align="center" style="background:LemonChiffon;"|SESSION 4<br>Theory & Practice|| align="center" style="background:LemonChiffon;"|Eyepieces<br>Depth of field<br> Depth of focus<br>more Koehler||align="center" style="background:LemonChiffon;"|BRITTA<br>BioDIP TEAM ||align="center" style="background:LemonChiffon;"|students microscopes with 10x/0.25 and 40x/0.65 objectives<br>Stereoscope with a "sample" | ||
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|style="background:LemonChiffon;"|17:30 | |style="background:LemonChiffon;"|17:30 | ||
| − | |style="background:LemonChiffon;"| | + | |style="background:LemonChiffon;"|18:00||align="center" style="background:LemonChiffon;"|SESSION 5<br>Practice<br>2 groups, 15min rotation<br>(13min at stations incl 2min for switching)<br>timer:SILKE<br>LAURE|| align="center" style="background:LemonChiffon;"| introduction to UC2<br>getting to know microscope parts<br>(one group takes the scopes apart, <br>the next one puts them back togetehr again)||align="center" style="background:LemonChiffon;"|SEBASTIAN<br>BioDIP TEAM ||align="center" style="background:LemonChiffon;"|UC2 box<br>two old microscopes (upright, inverted), screwdrivers |
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| − | + | |align="center" style="background:SkyBlue;"|'''19:00''' | |
| − | + | |align="center" style="background:SkyBlue;"|'''open end''' | |
| − | + | |align="center" style="background:SkyBlue;"|'''Dinner''' | |
| − | + | |align="center" style="background:SkyBlue;"|'''with all teachers'''|| align="center" style="background:SkyBlue;"|'''BioDIP TEAM'''|| align="center" style="background:SkyBlue;"|''' good mood, time''' | |
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|} | |} | ||
| − | === DAY TWO - Tue | + | === DAY TWO - Tue 24th March === |
organize pitchers with water and cups for short breaks | organize pitchers with water and cups for short breaks | ||
| Line 151: | Line 151: | ||
| 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 1 ||align="center" |BioDIP TEAM || align="center" | Questions<br>teaching microscopes; conjugate planes schemes |
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|- | |- | ||
| − | | | + | | style="background:mediumseagreen;"|'''10:00''' |
| + | | style="background:mediumseagreen;"|'''10:05''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | ||
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| − | |10: | + | |10:05||10:45||align="center"|SESSION 1a <br>DEMONSTRATION||align="center" | Diffraction and Diffraction slide fun<br> Diffraction string show ||align="center"|JAN || align="center" | diffraction slides, torch, "dashed" string, fabric, funny glasses |
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| − | + | |10:45||11:05||align="center"|SESSION 1b <br>THEORY||align="center" | Wave optics, Diffraction, and Resolution ||align="center"|BRITTA|| align="center" | "dashed" string | |
| − | | | + | |
|- | |- | ||
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| − | | style="background:mediumseagreen;"|''' | + | | style="background:mediumseagreen;"|'''11:05''' |
| − | | style="background:mediumseagreen;"|'''11: | + | | style="background:mediumseagreen;"|'''11:20''' |
|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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| − | |11: | + | |style="background:LemonChiffon;"| 11:20 |
| + | |style="background:LemonChiffon;"| 11:50 ||align="center" style="background:LemonChiffon;"|SESSION 1a<br>Practice<br> 2 groups, 15min Rotation <br>(10min at stations + 5min for switching in-between)<br>Timer: LAURE|| align="center" style="background:LemonChiffon;"|Interference and Diffraction||align="center" style="background:LemonChiffon;"|SEBASTIAN<br>BRITTA|| align="center" style="background:LemonChiffon;"| Mach-Zehnder interferometer demo setup<br> Ripple tank with various accessories | ||
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| − | | | + | | 11:20||12:30||align="center"| SESSION 1b <br> Demo and Theory || align="center"|ABBE's diffraction demonstration ||align="center" |LAURE <br> (SILKE) ||align="center" |Dan's ABBE Diffraction demo setup |
| − | + | ||
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| − | + | | style="background:mediumseagreen;"|'''12:30''' | |
| − | + | | style="background:mediumseagreen;"|'''13:30''' | |
| − | + | ||
| − | | style="background:mediumseagreen;"|''' | + | |
| − | | style="background:mediumseagreen;"|'''13: | + | |
|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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| − | |style="background:LemonChiffon;"| 13: | + | |style="background:LemonChiffon;"| 13:30 |
| − | |style="background:LemonChiffon;"| | + | |style="background:LemonChiffon;"| 13:50 ||align="center" style="background:LemonChiffon;"|SESSION 1b<br>Practice|| align="center" style="background:LemonChiffon;"|Diffraction hands on on student microscopes||align="center" style="background:LemonChiffon;"|BioDIP TEAM || align="center" style="background:LemonChiffon;"| rulers as gratings,<br> place holder for objective Nomarski prism, piece of card board, <br>microscopes without condenser, closed field diaphragm, <br>some small scissors would be nice |
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| − | | | + | | 13:50||14:00||align="center"|SESSION 1c<br> Theory ||align="center" | Wrap - up & Q & A <br>Diffraction ||align="center" |JAN <br>BioDIP TEAM|| |
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| − | | align="center"| | + | | align="center"|14:00 |
| − | |align="center"| | + | |align="center"|14:10||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Tobias Fürstenhaupt, Leader EM facility||align="center" |Tobias<br>(JAN)<br> was moved but do not know to when anymore|| align="center" | Q & A with Tobias about his facility and cooperation with LMF <br> cut magnetic copper coil (Tobias')| |
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| − | | 14: | + | | 14:10||14:45||align="center"|SESSION 2<br>Theory and Demo||align="center" | Lens abERRations and corrections<br>finite versus infinite tube length<br>objective labeling/reading ||align="center" |MICHAEL ZOELFFEL<br>JAN|| align="center" |lenses with various sizes and shapes |
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| − | | | + | | 14:45||14:55||align="center"|SESSION 3<br>Theory||align="center" | Objective reading<br> lateral vs angular magnification||align="center" |JAN<br>BRITTA || align="center" |objectives, eyepieces, overhead projector with digital source switch |
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| − | | | + | | 14:55||15:00||align="center"|SESSION 2 <br> Demo ||align="center" | demo of spherical aberration ||align="center" |SEBASTIAN||align="center"| magnetic lens + laser suitcase on white board |
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| − | + | | style="background:mediumseagreen;"|'''15:00''' | |
| − | + | | style="background:mediumseagreen;"|'''15:15''' | |
| − | + | ||
| − | + | ||
| − | | style="background:mediumseagreen;"|'''15: | + | |
| − | | style="background:mediumseagreen;"|''' | + | |
|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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| − | |style="background:LemonChiffon;"| | + | |style="background:LemonChiffon;"| 15:15 |
| − | |style="background:LemonChiffon;"|16: | + | |style="background:LemonChiffon;"|16:15||align="center" style="background:LemonChiffon;"|SESSION 3<br>Practice<br> 2 groups, 30min Rotation <br>(25min at stations + 5min for switching in-between)<br>Timer: LAURE||align="center" style="background:LemonChiffon;"| Cover glasses, sample mounting, Objective cleaning and <br> infinity optics bench demo<br>Objective reading ||align="center" style="background:LemonChiffon;"|JAN<br><br>BRITTA ||align="center" style="background:LemonChiffon;"| Coverglasses (High preciscion), different oils, slides, different cleaning reagents, glass waste bin, cover glass thickness measure meter<br>toilet paper and sand paper <br> bench demo of infinity optics <br> box with broken objectives + two 160 tube lens objectives<br>cell culture microscope with finite tube length |
| − | + | ||
| − | + | ||
| − | + | ||
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| − | | 16: | + | | 16:15||16:30||align="center"|SESSION 4<br>Theory||align="center" | Introduction to contrast ||align="center" |BRITTA || |
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| − | | | + | | 16:30 || 16:45 ||align="center"|SESSION 5a<br>Theory|| align="center"| Basics of Dark Field microscopy||align="center" |JAN ||align="center" |Zeiss reflection dark field condenser from W3 + new 100x iris objective<br> video with dark field example; from web and own |
| − | | | + | |
|- | |- | ||
|- | |- | ||
| − | | style="background:mediumseagreen;"|''' | + | | style="background:mediumseagreen;"|'''16:45''' |
| − | | style="background:mediumseagreen;"|''' | + | | style="background:mediumseagreen;"|'''16:55''' |
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| style="background:mediumseagreen;"|''' ''' ||align="center" style="background:mediumseagreen;" | | ||
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| − | | | + | |style="background:LemonChiffon;"| 16:55 |
| + | |style="background:LemonChiffon;"| 17:15 ||align="center" style="background:LemonChiffon;"|SESSION 5b<br>Practice|| align="center" style="background:LemonChiffon;"|Dark Field microscopy||align="center" style="background:LemonChiffon;"|BioDIP TEAM || align="center" style="background:LemonChiffon;"| diatom slides | ||
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| − | + | | 17:15 || 17:30 ||align="center"|SESSION 6a<br>Theory|| align="center"| Basics of Phase Contrast microscopy||align="center" |SEBASTIAN ||align="center"| including videos from web and own | |
|- | |- | ||
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| − | |align="center"| | + | |align="center"| 17:30 ||align="center"| 17:35 ||align="center"|SESSION 6b<br>Show & Tell|| align="center"| show parts needed to Phase Contrast in condenser and respective objective||align="center" |JAN ||align="center" |condenser with Phase annuli, phase contrast objective |
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| − | |style="background:LemonChiffon;"| | + | |align="center"| 17:35 ||align="center"| 17:40 ||align="center"|SESSION 7<br>Demonstration|| align="center"| Cheek cell prep||align="center" |JAN ||align="center" |Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
| − | |style="background:LemonChiffon;"|18: | + | |- |
| + | |- | ||
| + | |style="background:LemonChiffon;"| 17:40 | ||
| + | |style="background:LemonChiffon;"|18:00||align="center" style="background:LemonChiffon;"|SESSION 6c<br>Practice|| align="center" style="background:LemonChiffon;"|Phase Contrast microscopy ||align="center" style="background:LemonChiffon;"|BioDIP TEAM || align="center" style="background:LemonChiffon;"| diatomes and similar samples <br> cell culture microscope with cells in a dish as live example for phase contrast | ||
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|} | |} | ||
| − | === DAY THREE - Wed | + | === DAY THREE - Wed 25th March === |
organize pitchers with water and cups for short breaks | organize pitchers with water and cups for short breaks | ||
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|align="center" style="background:mediumseagreen;"|'''10:00''' | |align="center" style="background:mediumseagreen;"|'''10:00''' | ||
| − | |align="center" style="background:mediumseagreen;"|'''10: | + | |align="center" style="background:mediumseagreen;"|'''10:10''' |
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | ||
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| − | | align="center"|10: | + | | align="center"|10:10||align="center"|10:25||align="center"|SESSION 1<br>Demonstration||align="center" | Polarized light microscopy||align="center" |JAN ||align="center"|for students and Sebastian: calcite crystal blocks, polarizers, paper with black spot;<br>overhead projector<br>stone samples, gummy bears, plastic dishes, plastic rulers... |
|- | |- | ||
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| − | | align="center"|10: | + | | align="center"|10:25||align="center"|11:10||align="center"|SESSION 1<br>Theory and Demo||align="center" | Polarized light microscopy||align="center" |SEBASTIAN<br>JAN ||align="center"|cell image library video<br>info about LC-PolScope from openpolscope.org/<br>introduce responsible person for Brugues' PolScope<br>pol scope with rotatable stage |
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| − | |align="center" style="background:LemonChiffon;"| 11: | + | |align="center" style="background:LemonChiffon;"| 11:10 |
| − | |align="center" style="background:LemonChiffon;"|11: | + | |align="center" style="background:LemonChiffon;"|11:30||align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice||align="center" style="background:LemonChiffon;"| Polarized light microscopy||align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"| hair, stone samples, benzocain crystals, tissue pieces ... |
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| − | |align="center" style="background:mediumseagreen;"|'''11: | + | |align="center" style="background:mediumseagreen;"|'''11:30''' |
|align="center" style="background:mediumseagreen;"|'''11:45''' | |align="center" style="background:mediumseagreen;"|'''11:45''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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| − | |align="center" style="background:LemonChiffon;"| | + | |16:55||17:05||align="center"|SESSION 4f<br>Theory||align="center" | Epi illumination||align="center" |JAN || |
| − | |align="center" style="background:LemonChiffon;"| 18:00||align="center" style="background:LemonChiffon;"|SESSION | + | |- |
| + | |- | ||
| + | |align="center" style="background:LemonChiffon;"| 17:05 | ||
| + | |align="center" style="background:LemonChiffon;"| 18:00||align="center" style="background:LemonChiffon;"|SESSION 4g<br>Practice|| align="center" style="background:LemonChiffon;"|Spectraviewer<br>Fluorescence imaging at microscopes|| align="center" style="background:LemonChiffon;"|SEBASTIAN<br>BioDIP TEAM|| align="center" style="background:LemonChiffon;"|laminated sheets with DAPI/FITC/TRITC Spectra <br> red, green, blue, board markers<br> EtOH spray bottles + tissue<br> Fluorescent labeled samples (Convalaria) | ||
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|} | |} | ||
| − | === DAY FOUR - Thu | + | === DAY FOUR - Thu March 26th === |
organize pitchers with water and cups for short breaks | organize pitchers with water and cups for short breaks | ||
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| − | |align="center"|10:00||align="center"|10: | + | |align="center" style="background:mediumseagreen;"|'''10:00''' |
| + | |align="center" style="background:mediumseagreen;"|'''10:05''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |- | ||
| + | |- | ||
| + | |align="center"|10:05||align="center"|10:40||align="center"|SESSION 1<br> Theory ||align="center" | Fluorophores ||align="center" |SEBASTIAN ||align="center" |-||align="center" |Molecular probes catalogue | ||
| + | |- | ||
| + | |- | ||
| + | |align="center"|10:40||align="center"|10:50||align="center"|SESSION 2a<br>Demo|| align="center"|Detectors ||align="center" |BRITTA<br>JAN||align="center" |showing different chip sizes||align="center" | CCD chip paper weight <br>Demo: CCD chip under stereo microscope <br>example cameras with differently sized chips | ||
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| − | |align="center" style="background:mediumseagreen;"|'''10: | + | |align="center" style="background:mediumseagreen;"|'''10:50''' |
| − | |align="center" style="background:mediumseagreen;"|''' | + | |align="center" style="background:mediumseagreen;"|'''11:00''' |
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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| − | | | + | |11:00||12:00||align="center"|SESSION <br>THEORY||align="center" | SEMINAR ||align="center"|Lecturer<br>Markus Sauer|| align="center" | || |
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| − | |align="center" | + | |align="center" style="background:mediumseagreen;"|'''12:00''' |
| + | |align="center" style="background:mediumseagreen;"|'''12:10''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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| − | |align="center"| | + | |align="center"|12:10||align="center"|12:50||align="center"|SESSION 2b<br>Theory|| align="center"|Detectors ||align="center" |BRITTA||align="center" |showing overflow with water and beakers||align="center" | 3 different sized beakers<br> + big one<br>+ one filled with water |
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| − | |align="center" style="background: | + | |align="center" style="background:mediumseagreen;"|'''12:50''' |
| − | |align="center" style="background: | + | |align="center" style="background:mediumseagreen;"|'''13:30''' |
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" style="background:mediumseagreen;"|'''LUNCH''' | ||
|- | |- | ||
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| − | |align="center" | + | |align="center"|13:30||align="center"|13:40||align="center"|SESSION 2c<br>Demo|| align="center"|Detectors ||align="center" |BRITTA||align="center" |bench show||align="center" | RT spot with RGB slider and camera objective<br> PC<br> nice sample for binning (coffee cup)<br>show grid at AC outlet in room |
| − | |align="center" | + | |
| − | |align="center | + | |
| − | |align="center | + | |
|- | |- | ||
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| − | |align="center" | | + | |align="center"|13:40||align="center"|13:55||align="center"|SESSION 2d<br>Theory|| align="center"|Detectors ||align="center" |BRITTA||align="center" |advanced detectors lecture||align="center" | |
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| − | |align="center" | + | |align="center" style="background:LemonChiffon;"|13:55 |
| + | |align="center" style="background:LemonChiffon;"|14:00||align="center" style="background:LemonChiffon;"|SESSION 2e<br>Practice||align="center" style="background:LemonChiffon;"|Detectors<br>"QE" show ||align="center" style="background:LemonChiffon;"|JAN||align="center" style="background:LemonChiffon;"|students count times of laser pointer blinking||align="center" style="background:LemonChiffon;" |blinking laser pointer | ||
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| − | |align="center" | + | |align="center" |14:00 ||align="center"|14:25||align="center"|SESSION 3a<br>Theory|| align="center"|Digital images ||align="center" |LAURE||align="center" |Nyquist-Shannon<br>what is a pixel<br>spatial calibration||align="center" | comment about difference noise and background (unspecific) signal |
| − | |align="center | + | |
|- | |- | ||
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| − | |align="center" | + | |align="center" |14:25 ||align="center"|14:30||align="center"|SESSION 3a<br>Demo|| align="center"|Digital images ||align="center" |JAN||align="center" |Nyquist-Shannon<br>spatial calibration||align="center" | overhead projector<br>sheets with different sized squares as example for dexel size<br>gummi bears, Sesame seeds |
| − | |align="center | + | |
|- | |- | ||
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| − | | align="center" | + | |align="center" style="background:LemonChiffon;"|14:30 |
| + | |align="center" style="background:LemonChiffon;"|14:45|| align="center" style="background:LemonChiffon;"|SESSION 3a<br>Practice|| align="center" style="background:LemonChiffon;"|calculating dexel/pixel size|| align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"|practice calculating needed dexel size for given optical setup || align="center" style="background:LemonChiffon;"|calculator<br>text with given optical setup (within Bert's presentation) | ||
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| − | |align="center" style="background: | + | |align="center" style="background:LemonChiffon;"|14:45 |
| − | |align="center" style="background: | + | |align="center" style="background:LemonChiffon;"|14:50|| align="center" style="background:LemonChiffon;"|SESSION 3a<br>Practice|| align="center" style="background:LemonChiffon;"|calculating dexel/pixel size|| align="center" style="background:LemonChiffon;"|LAURE|| align="center" style="background:LemonChiffon;"|practice calculating needed dexel size for given optical setup || align="center" style="background:LemonChiffon;"|evaluation of the results from practical plus more calculation examples |
| − | |align="center" style="background: | + | |
| − | |align="center" style="background: | + | |
|- | |- | ||
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| − | |align="center | + | | align="center"|14:50||align="center"|15:15||align="center"|SESSION 3b<br>Theory|| align="center"|Quantitative Imaging ||align="center" |LAURE||align="center" |digitization in space, (time) & intensity<br>aliasing ||align="center" |- |
| − | |align="center | + | |
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| − | |align="center" style="background:mediumseagreen;"|'''15: | + | |align="center" style="background:mediumseagreen;"|'''15:15''' |
| − | |align="center" style="background:mediumseagreen;"|'''15: | + | |align="center" style="background:mediumseagreen;"|'''15:25''' |
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' | |align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' | ||
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| − | | align="center"|15: | + | |align="center" style="background:LemonChiffon;"|15:25 |
| − | |align="center"| | + | |align="center" style="background:LemonChiffon;"|16:25|| align="center" style="background:LemonChiffon;"|SESSION 4<br>Practice|| align="center" style="background:LemonChiffon;"|discussion and practice imaging with CCD/CMOS cameras 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<br> LUT, saturation, histogram etc|| align="center" style="background:LemonChiffon;"|camera spec sheets (in microscope handbook at each teaching scope)<br>Hamamatsu camera comparison list (extra sheet) <br>camera vocabulary checklist (in microscope handbook at each teaching scope) <br> microscope ruler<br>Fluorescence Sample slides (Kidney / Cells...) |
|- | |- | ||
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| − | |align="center" | | + | |align="center" |16:25||align="center"|16:35||align="center"|SESSION 5a<br>Theory ||align="center" | OPTICAL SECTIONING<br>introduction<br>widefield & deconvolution||align="center" |JAN||align="center"|-||align="center" |labtop |
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| − | |align="center" | | + | |align="center" |16:35||align="center"|16:45||align="center"|SESSION 6<br>Theory ||align="center" | CHROMATIC ABERRATION||align="center" |JAN|| ||align="center" | |
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| − | |||
| − | |||
| − | |||
| − | |||
|align="center" style="background:mediumseagreen;"|'''16:45''' | |align="center" style="background:mediumseagreen;"|'''16:45''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''16:50''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| − | |align="center" style="background:mediumseagreen;"|'''BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' | + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' |
|- | |- | ||
| + | |align="center"|16:50||align="center"|17:20||align="center"|SESSION 5b<br>Theory & Demo ||align="center" | OPTICAL SECTIONING<br>Laser Scanning Confocal||align="center" |JAN||||align="center"|"confocal equipment": <br> laser pointer, mirror, broken scanning mirror | ||
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| − | |||
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| + | |align="center" |17:20||align="center"|17:50||align="center"|SESSION 5c<br>Theory& Demo ||align="center" | OPTICAL SECTIONING<br>2-Photon Microscopy ||align="center" |SEBASTIAN<br>JAN||||align="center"|dual laser pointer (blue, green, red)<br> piece of cheese <br>to demonstrate penetration of diff. wavelength | ||
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| − | |||
|- | |- | ||
| + | |align="center"|17:50||align="center"|18:15||align="center"|SESSION 5d<br>Theory ||align="center" | OPTICAL SECTIONING<br>Spinning Disc Confocal||align="center" |BRITTA<br>JAN||||align="center"|beer bottle from Plzen | ||
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| − | |align="center"| | + | |- |
| + | |align="center" style="background:LemonChiffon;"|18:15||align="center" style="background:LemonChiffon;"|18:35||align="center" style="background:LemonChiffon;"|SESSION 5d<br>DEMO, voluntary<br>2 groups, 10min rotation<br>(8min at stations + 2min for switching)<br>timer: LAURE, BRITTA ||align="center" style="background:LemonChiffon;"| OPTICAL SECTIONING<br>Spinning Disc Confocal||align="center" style="background:LemonChiffon;"|JAN<br>SEBASTIAN||align="center" style="background:LemonChiffon;"| ||align="center" style="background:LemonChiffon;"|DAN's "spinning-disc-on-a-bench"<br>UC2 spinning disc system | ||
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|- | |- | ||
|} | |} | ||
| − | === DAY FIVE - Fri | + | === DAY FIVE - Fri March 27th === |
organize pitchers with water and cups for short breaks | organize pitchers with water and cups for short breaks | ||
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| align="center" style="background:#f0f0f0; width:25%"|'''Materials needed''' | | align="center" style="background:#f0f0f0; width:25%"|'''Materials needed''' | ||
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| − | |align="center"|9:00||align="center"|10: | + | |align="center"|9:00||align="center"|10:00||align="center"|Recap ||align="center" | day 4 ||align="center" |BioDIP TEAM||align="center"|Question sheets with the real case problem<br>calculators, pens<br>voting kit? |
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| − | |align="center" style="background:mediumseagreen;"|'''10: | + | |align="center" style="background:mediumseagreen;"|'''10:00''' |
| − | |align="center" style="background:mediumseagreen;"|'''10: | + | |align="center" style="background:mediumseagreen;"|'''10:10''' |
|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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| − | |align="center" |10: | + | |align="center" |10:10||align="center"|10:25||align="center"|SESSION 1a<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>TIRF ||align="center" |BRITTA ||align="center" |big plastic cuvette tank filled with water<br>+ red and green laser pointer |
|- | |- | ||
|- | |- | ||
| − | |align="center"|10: | + | |align="center"|10:25||align="center"|10:45||align="center"|SESSION 1b<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |SEBASTIAN ||align="center" |glass block with brain/scull and red light sheet laser from ZEISS |
|- | |- | ||
|- | |- | ||
| − | |align="center"|10: | + | |align="center"|10:45||align="center"|11:05||align="center"|SESSION 1c<br>Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |SEBASTIAN <br>(JOHANNES)||align="center" |PETE's SPIM-in-a-suitcase |
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| − | |align="center"|11: | + | |align="center"|11:05||align="center"|11:10||align="center"|SESSION 1d<br>Theory||align="center" | OPTICAL SECTIONING<br>Apotome ||align="center" |JAN ||align="center" | |
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| − | |align="center"|11: | + | |align="center"|11:10||align="center"|11:20||align="center"|SESSION 1e<br>Theory||align="center" | OPTICAL SECTIONING<br>final remarks ||align="center" |JAN ||align="center" | |
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| − | |align="center" style="background:mediumseagreen;"|'''11: | + | |align="center" style="background:mediumseagreen;"|'''11:20''' |
| − | |align="center" style="background:mediumseagreen;"|'''11: | + | |align="center" style="background:mediumseagreen;"|'''11:35''' |
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' | |align="center" style="background:mediumseagreen;"|'''BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' | ||
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| − | |align="center"|11: | + | |align="center"|11:35||align="center"|12:10||align="center"|SESSION 2a<br>Theory||align="center" | EXTENDED RESOLUTION<br>SIM<br>SMLM ||align="center" |LAURE ||align="center" | |
|- | |- | ||
|- | |- | ||
| − | |align="center"|12: | + | |align="center"|12:10||align="center"|12:35||align="center"|SESSION 2b<br>Theory||align="center" | EXTENDED RESOLUTION<br>STED<br>Airyscan/Pixel reassignment<br>Sample Preparation ||align="center" |LAURE ||align="center" | |
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| − | |align="center"|12: | + | |align="center"|12:35||align="center"|12:45||align="center"|DISCUSSION||align="center"| preparation for Monday hands-on sessions||align="center" |SEBASTIAN<br>BioDIP team ||align="center" |white board |
|- | |- | ||
|align="center" style="background:mediumseagreen;"|'''12:45''' | |align="center" style="background:mediumseagreen;"|'''12:45''' | ||
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| − | |align="center"|13:30||align="center"|13: | + | |align="center"|13:30||align="center"|13:40||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Riccardo Maraspini - Honigmann-lab (STED)||align="center" |RICCARDO<br>(JAN)|| align="center" | Q & A with Riccardo about Honigmann lab, STED, and cooperation possibilities |
| + | |- | ||
| + | |- | ||
| + | | align="center"|13:40 | ||
| + | |align="center"|13:50||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Hella Hartmann, BioDIP Coordinator||align="center" |HELLA<br>(JAN)|| align="center" | Q & A with HELLA about BioDIP and cooperation between the participating facilities<br> BioDIP website | ||
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| − | |align="center"|13: | + | |align="center"|13:50||align="center"|14:00||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Noreen Walker, Leader Scientific Computing facility||align="center" |NOREEN<br>(JAN)|| align="center" | introduction to bioinformatics service and image processing facility |
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| − | |align="center"| | + | |align="center"|14:00||align="center"|14:10||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Nicola Maghelli, Leader Advanced Imaging Facility||align="center" |NICOLA<br>(JAN)|| align="center" | introduction to Advanced Imaging Facility |
|- | |- | ||
|- | |- | ||
| − | |align="center"|14: | + | |align="center"|14:10||align="center"|14:20||align="center"|SESSION 3|| align="center"|Planning your Imaging Experiment ||align="center" |JAN<br>(LAURE)||align="center" | + introduction to new user project questions |
|- | |- | ||
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| − | |align="center"|14: | + | |align="center"|14:20||align="center"|14:35||align="center"|SESSION 4<br>Therory & Discussion|| align="center"|Controls in microcsopy ||align="center" |LAURE||align="center" |discussion about why controls are needed, what needs to be checked |
|- | |- | ||
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| − | |align="center"|14: | + | |align="center"|14:35||align="center"|14:55||align="center"|SESSION 5<br> Project discussion|| align="center"|One volunteer presents his/her imaging problem shortly <br>and discuss it with the whole group ||align="center" |BioDIP TEAM <br>+ NOREEN||align="center" |NOTE: ask for a volunteer already on Monday, than again on Wednesday |
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|} | |} | ||
| − | === DAY SIX - optional - Mon | + | === DAY SIX - optional - Mon 30th March afternoon=== |
{| border="4" cellpadding="2" cellspacing="8" {| {{table}} | {| border="4" cellpadding="2" cellspacing="8" {| {{table}} | ||
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| − | |align="center"|13:00||align="center" |13:45||align="center"|Preparation for hands-on ||align="center" | OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" | BioDIP team ||align="center" |MZ1, LZ2, CZ6, SD4, | + | |align="center"|13:00||align="center" |13:45||align="center"|Preparation for hands-on ||align="center" | OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" | BioDIP team ||align="center" |MZ1, LZ2, CZ6, SD4, H4, H2; UC2<br> we need to decide which systems to use<br> also block W7 |
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| − | |align="center" |14:00||align="center" |15:30||align="center"|SESSION I<br> hands-on||align="center" | OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" |BioDIP team ||align="center" |MZ1, LZ2, CZ6, SD4, | + | |align="center" |14:00||align="center" |15:30||align="center"|SESSION I<br> hands-on||align="center" | OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" |BioDIP team ||align="center" |MZ1, LZ2, CZ6, SD4, H4, H2<br>potentially UC2 |
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| − | |align="center" |16:00||align="center" |17:30||align="center"|SESSION II<br>hands-on|| align="center"|OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" |BioDIP TEAM||align="center" |MZ1, LZ2, CZ6, SD4, | + | |align="center" |16:00||align="center" |17:30||align="center"|SESSION II<br>hands-on|| align="center"|OPTICAL SECTIONING / EXTENDED RESOLUTION ||align="center" |BioDIP TEAM||align="center" |MZ1, LZ2, CZ6, SD4, H4, H2<br>potentially UC2 |
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|align="center" |17:30||align="center" |18:00||align="center"|ROUND-UP|| align="center"|FINAL GET TOGETHER||align="center" |BioDIP TEAM||align="center" |LMF office or atrium | |align="center" |17:30||align="center" |18:00||align="center"|ROUND-UP|| align="center"|FINAL GET TOGETHER||align="center" |BioDIP TEAM||align="center" |LMF office or atrium | ||
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Latest revision as of 11:38, 27 February 2020
Contents |
[edit] PhD Program: Basics of Light Microscopy - LMF - Course March 2020
[edit] Tentative Schedule
[edit] SETUP - Thu March 19th and Fri March 20th
Again in CSBD SR top floor, also using landing in front of it
Room is reserved from (incl) Thu, March 19th 2020 4:00PM - Tues, March 31st, 5PM!
Mon March 30th and Tue March 31st is basically to have room blocked for Building maintenance to put back all tables and chairs
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 Thurs afternoon and Friday morning, can already start We afternoon/ Thu 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
- Flash lights (check batteries!)
- 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!)
[edit] DAY ONE - Mon 23rd March
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; ask students for volunteering for Friday's project discussion round (we need two - three volunteers) |
| 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 1 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 | 10:35 | BREAK | BREAK | ||
| 10:35 | 11:20 | SESSION 1 Practice 3 groups, 15min Rotation (12min at stations + 3min for switching in-between) 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 (take from Tuesday box!) *refractometer |
| 11:20 | 12:00 | SESSION 1d Theory |
Introduction to lenses and objectives Magnification |
JAN | cut objective foam objective |
| 12:00 | 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 (pizza or cake) |
| 12:05 | 13:00 | LUNCH | LUNCH | ||
| 13:00 | 13:45 | SESSION 1 Practice 3 groups, 15min Rotation (12min at stations + 3min for switching in-between) Timer: SEBASTIAN SILKE |
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 |
MICHAEL ZOELFFEL JAN |
|
| 14:25 | 14:45 | BREAK | BREAK | ||
| 14:45 | 15:45 | SESSION 2 Practice 2 groups, 30min Rotation (27min at stations + 3min for switching in-between) Timer: SEBASTIAN SILKE |
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 |
| 15:45 | 16:00 | SESSION 3 Theory |
Koehler illumination (Microscope alignment) |
MICHAEL ZOELFFEL JAN |
|
| 16:00 | 16:20 | BREAK | BREAK | ||
| 16:20 | 17:20 | SESSION 3a Practice |
Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
| 17:20 | 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 | 18:00 | SESSION 5 Practice 2 groups, 15min rotation (13min at stations incl 2min for switching) timer:SILKE LAURE |
introduction to UC2 getting to know microscope parts (one group takes the scopes apart, the next one puts them back togetehr again) |
SEBASTIAN BioDIP TEAM |
UC2 box two old microscopes (upright, inverted), screwdrivers |
| 19:00 | open end | Dinner | with all teachers | BioDIP TEAM | good mood, time |
[edit] DAY TWO - Tue 24th March
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 | 10:45 | SESSION 1a DEMONSTRATION |
Diffraction and Diffraction slide fun Diffraction string show |
JAN | diffraction slides, torch, "dashed" string, fabric, funny glasses |
| 10:45 | 11:05 | SESSION 1b THEORY |
Wave optics, Diffraction, and Resolution | BRITTA | "dashed" string |
| 11:05 | 11:20 | BREAK | COFFEE BREAK | ||
| 11:20 | 11:50 | SESSION 1a Practice 2 groups, 15min Rotation (10min at stations + 5min for switching in-between) Timer: LAURE |
Interference and Diffraction | SEBASTIAN BRITTA |
Mach-Zehnder interferometer demo setup Ripple tank with various accessories |
| 11:20 | 12:30 | SESSION 1b Demo and Theory |
ABBE's diffraction demonstration | LAURE (SILKE) |
Dan's ABBE Diffraction demo setup |
| 12:30 | 13:30 | BREAK | LUNCH | ||
| 13:30 | 13:50 | 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 |
| 13:50 | 14:00 | SESSION 1c Theory |
Wrap - up & Q & A Diffraction |
JAN BioDIP TEAM |
|
| 14:00 | 14:10 | SESSION Meet & Greet |
Meeting Tobias Fürstenhaupt, Leader EM facility | Tobias (JAN) was moved but do not know to when anymore |
Q & A with Tobias about his facility and cooperation with LMF cut magnetic copper coil (Tobias')| |
| 14:10 | 14:45 | SESSION 2 Theory and Demo |
Lens abERRations and corrections finite versus infinite tube length objective labeling/reading |
MICHAEL ZOELFFEL JAN |
lenses with various sizes and shapes |
| 14:45 | 14:55 | SESSION 3 Theory |
Objective reading lateral vs angular magnification |
JAN BRITTA |
objectives, eyepieces, overhead projector with digital source switch |
| 14:55 | 15:00 | SESSION 2 Demo |
demo of spherical aberration | SEBASTIAN | magnetic lens + laser suitcase on white board |
| 15:00 | 15:15 | BREAK | COFFEE BREAK | ||
| 15:15 | 16:15 | SESSION 3 Practice 2 groups, 30min Rotation (25min at stations + 5min for switching in-between) Timer: LAURE |
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 |
| 16:15 | 16:30 | SESSION 4 Theory |
Introduction to contrast | BRITTA | |
| 16:30 | 16:45 | 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 |
| 16:45 | 16:55 | BREAK | SHORT BREAK | ||
| 16:55 | 17:15 | SESSION 5b Practice |
Dark Field microscopy | BioDIP TEAM | diatom slides |
| 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 | JAN | Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
| 17:40 | 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 |
[edit] DAY THREE - Wed 25th March
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 | 10:10 | 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, plastic rulers... |
| 10:25 | 11:10 | 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 |
| 11:10 | 11:30 | SESSION 1 Practice |
Polarized light microscopy | BioDIP TEAM | hair, stone samples, benzocain crystals, tissue pieces ... |
| 11:30 | 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 |
BRITTA | • 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. |
BRITTA LAURE |
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 |
BRITTA LAURE |
|
| 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 | 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) |
[edit] DAY FOUR - Thu March 26th
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 | 10:40 | SESSION 1 Theory |
Fluorophores | SEBASTIAN | - | Molecular probes catalogue |
| 10:40 | 10:50 | 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 |
| 10:50 | 11:00 | BREAK | SHORT BREAK | BREAK | BREAK | BREAK |
| 11:00 | 12:00 | SESSION THEORY |
SEMINAR | Lecturer Markus Sauer |
||
| 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 | RT spot with RGB slider and camera objective PC nice sample for binning (coffee cup) show grid at AC outlet in room |
| 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 | LAURE | 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 | LAURE | 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 |
Quantitative Imaging | LAURE | 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 / Cells...) |
| 16:25 | 16:35 | SESSION 5a Theory |
OPTICAL SECTIONING introduction widefield & deconvolution |
JAN | - | labtop |
| 16:35 | 16:45 | SESSION 6 Theory |
CHROMATIC ABERRATION | 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: LAURE, BRITTA |
OPTICAL SECTIONING Spinning Disc Confocal |
JAN SEBASTIAN |
DAN's "spinning-disc-on-a-bench" UC2 spinning disc system |
[edit] DAY FIVE - Fri March 27th
organize pitchers with water and cups for short breaks
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 10:00 | Recap | day 4 | BioDIP TEAM | Question sheets with the real case problem calculators, pens voting kit? |
| 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 water + red and green laser pointer |
| 10:25 | 10:45 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING SPIM |
SEBASTIAN | glass block with brain/scull and red light sheet laser from ZEISS |
| 10:45 | 11:05 | SESSION 1c Demo |
OPTICAL SECTIONING SPIM |
SEBASTIAN (JOHANNES) |
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 |
LAURE | |
| 12:10 | 12:35 | SESSION 2b Theory |
EXTENDED RESOLUTION STED Airyscan/Pixel reassignment Sample Preparation |
LAURE | |
| 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 Riccardo Maraspini - Honigmann-lab (STED) | RICCARDO (JAN) |
Q & A with Riccardo about Honigmann lab, 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 Noreen Walker, Leader Scientific Computing facility | NOREEN (JAN) |
introduction to bioinformatics service and image processing facility |
| 14:00 | 14:10 | SESSION Meet & Greet |
Meeting Nicola Maghelli, Leader Advanced Imaging Facility | NICOLA (JAN) |
introduction to Advanced Imaging Facility |
| 14:10 | 14:20 | SESSION 3 | Planning your Imaging Experiment | JAN (LAURE) |
+ introduction to new user project questions |
| 14:20 | 14:35 | SESSION 4 Therory & Discussion |
Controls in microcsopy | LAURE | discussion about why controls are needed, what needs to be checked |
| 14:35 | 14:55 | SESSION 5 Project discussion |
One volunteer presents his/her imaging problem shortly and discuss it with the whole group |
BioDIP TEAM + NOREEN |
NOTE: ask for a volunteer already on Monday, than again on Wednesday |
| 14:55 | 15:05 | BREAK | SHORT BREAK | BREAK | |
| 15:05 | 16:00 | SESSION 5 | Course evaluation | BioDIP TEAM | Gummy bear bags and/or fruits white board + marker |
[edit] DAY SIX - optional - Mon 30th March 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, H4, H2; UC2 we need to decide which systems to use also block W7 |
| 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, H4, H2 potentially UC2 |
| 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, H4, H2 potentially UC2 |
| 17:30 | 18:00 | ROUND-UP | FINAL GET TOGETHER | BioDIP TEAM | LMF office or atrium |
