BasicCoursePhDProg - Peter Evennett - schedule December 2016
From BioDIP
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(→DAY THREE - Wed 7th December: schedule updated with short break until lunch break) |
(→DAY THREE - Wed 7th December: added MZ interferometer setup to Polarisation and DIC theory parts) |
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|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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| − | | 11:05||11: | + | |style="background:LemonChiffon;"| 11:05 |
| + | |style="background:LemonChiffon;"| 11:25 ||align="center" style="background:LemonChiffon;"|SESSION 1a<br>Practice Round<br>Group rotation<br>(10min each)|| align="center" style="background:LemonChiffon;"|Interference and Diffraction||align="center" style="background:LemonChiffon;"|DAVIDE<br>BRITTA|| align="center" style="background:LemonChiffon;"| Mach-Zehnder interferometer demo setup<br> Ripple tank with various accessories | ||
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| + | | 11:25||11:50||align="center"| SESSION 1b <br> Demo and Theory || align="center"|ABBE's diffraction demonstration ||align="center" |BERT ||align="center" |Dan's ABBE Diffraction demo setup | ||
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| − | |style="background:LemonChiffon;"| 11: | + | |style="background:LemonChiffon;"| 11:50 |
| − | |style="background:LemonChiffon;"| 12: | + | |style="background:LemonChiffon;"| 12:20 ||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, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm, some small scissors would be nice |
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| − | | 12: | + | | 12:20||12:35||align="center"|SESSION 1c<br> Theory ||align="center" | Wrap - up & Q & A <br>Diffraction ||align="center" |PETER EVENNETT <br> JAN|| |
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| − | | style="background:mediumseagreen;"|'''12: | + | | style="background:mediumseagreen;"|'''12:35''' |
| style="background:mediumseagreen;"|'''13:15''' | | style="background:mediumseagreen;"|'''13:15''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
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| align="center" style="background:#f0f0f0; width:30%"|'''Materials needed''' | | align="center" style="background:#f0f0f0; width:30%"|'''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 2 ||align="center" |BioDIP TEAM || align="center" |Questions, pair of sieves, torches, microscopes |
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| − | | align="center"|10:30||align="center"|11:10||align="center"|SESSION 1<br>Theory||align="center" | Polarized light microscopy||align="center" |SEBASTIAN ||align="center"|info about LC-PolScope from openpolscope.org/<br>introduce responsible person for Brugues' PolScope | + | | align="center"|10:30||align="center"|11:10||align="center"|SESSION 1<br>Theory and Demo||align="center" | Polarized light microscopy||align="center" |SEBASTIAN ||align="center"|Mach-Zehnder interferometer setup |
| + | |-<br>info about LC-PolScope from openpolscope.org/<br>introduce responsible person for Brugues' PolScope | ||
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| + | |align="center" style="background:LemonChiffon;"| 11:10 | ||
| + | |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: | + | |align="center" style="background:mediumseagreen;"|'''11:30''' |
| + | |align="center" style="background:mediumseagreen;"|'''11:45''' | ||
|align="center" style="background:mediumseagreen;"|'''BREAK''' | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
|align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | |align="center" style="background:mediumseagreen;"|'''COFFEE BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | ||
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| − | + | |align="center"| 11:45||align="center"|12:20||align="center"|SESSION 2<br>Theory and Demo|| align="center"|Differential Interference Contrast (DIC)||align="center" |BRITTA ||Mach-Zehnder interferometer setup | |
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| − | |align="center"| 11:45||align="center"|12:20||align="center"|SESSION 2<br>Theory|| align="center"|Differential Interference Contrast (DIC)||align="center" |BRITTA || | + | |
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| − | |align="center"|14:30||align="center"|14: | + | |align="center"|14:30||align="center"|14:55||align="center"|SESSION 3<br>Theory||align="center" | Fundamental concepts of fluorescence ||align="center" |JAN||align="center" |fluorescent liquids in bottles plus laser pointer (blue, green, red; need stronger red + green ones!)<br>(in seminar room for darkness) |
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| − | |align="center"| 14: | + | |align="center"| 14:55||align="center"|15:35||align="center"|SESSION 4a<br>Theory + Demo||align="center" | Introduction to fluorescence microscopes<br>and light sources ||align="center" |DAVIDE<br>JAN||align="center" |• Light sources<br>• Lamp houses |
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|align="center" style="background:mediumseagreen;"|'''15:50''' | |align="center" style="background:mediumseagreen;"|'''15:50''' | ||
|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;"|'''COFFEE BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK'''|| align="center" style="background:mediumseagreen;"| |
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| − | |align="center" style="background: | + | |align="center" style="background:mediumseagreen;"|'''16:50''' |
| − | |align="center" style="background:LemonChiffon;"| 18: | + | |align="center" style="background:mediumseagreen;"|'''16:55''' |
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | ||
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| + | |align="center" style="background:LemonChiffon;"| 16:55 | ||
| + | |align="center" style="background:LemonChiffon;"| 18:05||align="center" style="background:LemonChiffon;"|SESSION 4e<br>Practice|| align="center" style="background:LemonChiffon;"|Spectraviewer<br>Aligment of Mercury arc lamps<br>Fluorescence imaging at microscopes|| align="center" style="background:LemonChiffon;"|JAN<br>BioDIP TEAM|| align="center" style="background:LemonChiffon;"|lamp house, screw driver<br>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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|align="center"|9:00||align="center"|10:00||align="center"|Recap ||align="center" | day 3 ||align="center" |BioDIP TEAM ||align="center" |-||align="center" |Questions (need to be adjusted to new course scheme!) | |align="center"|9:00||align="center"|10:00||align="center"|Recap ||align="center" | day 3 ||align="center" |BioDIP TEAM ||align="center" |-||align="center" |Questions (need to be adjusted to new course scheme!) | ||
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| + | |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''' | ||
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| − | |align="center | + | |align="center"|10:45||align="center"|11:10||align="center"|SESSION 2<br>Demo & Theory|| align="center"|Detectors ||align="center" |BRITTA||align="center" |bench show<br>advacned detectors lecture||align="center" | RT spot with RGB slider and camera objective<br> PC<br> nice sample for binning (coffee cup) |
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| − | |align="center"|11: | + | |align="center" style="background:LemonChiffon;"|11:10 |
| + | |align="center" style="background:LemonChiffon;"|11:25||align="center" style="background:LemonChiffon;"|SESSION 2<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" style="background: | + | |align="center" style="background:mediumseagreen;"|'''11:25''' |
| − | |align="center" style="background: | + | |align="center" style="background:mediumseagreen;"|'''11:40''' |
| + | |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;"|'''BREAK''' | ||
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| − | |align="center | + | |align="center" |11:55 ||align="center"|12:00||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 |
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| − | | align="center"| | + | |align="center" style="background:LemonChiffon;"|12:0 |
| − | |align="center"| | + | |align="center" style="background:LemonChiffon;"|12:25|| 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" | + | |align="center" style="background:LemonChiffon;"|12:25 |
| + | |align="center" style="background:LemonChiffon;"|12:35|| align="center" style="background:LemonChiffon;"|SESSION 3a<br>Practice|| align="center" style="background:LemonChiffon;"|calculating dexel/pixel size|| align="center" style="background:LemonChiffon;"|BERT|| 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 | ||
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| − | |align="center" style="background: | + | |align="center" style="background:mediumseagreen;"|'''12:35''' |
| − | |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 | + | |align="center"|13:35||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Tobias Fürstenhaupt, Leader EM facility||align="center" |Tobias<br>(JAN)|| align="center" | Q & A with Tobias about his facility and cooperation with LMF|| align="center"| - |
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| − | | align="center"|13: | + | | align="center"|13:35||align="center"|13:45||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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| − | |align="center" style="background:LemonChiffon;"|13: | + | |align="center" style="background:LemonChiffon;"|13:45 |
|align="center" style="background:LemonChiffon;"|15:10|| 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...) | |align="center" style="background:LemonChiffon;"|15:10|| 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" style="background:mediumseagreen;"|'''15:25''' | |align="center" style="background:mediumseagreen;"|'''15:25''' | ||
|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;"|'''COFFEE BREAK'''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' '''|| style="background:mediumseagreen;"|''' ''' |
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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"|10:05||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;"|'''10:05''' | ||
| + | |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;" | | ||
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| − | |align="center" style="background:mediumseagreen;"|''' | + | |align="center"|10:50||align="center"|11:00||align="center"|SESSION 1c<br>Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |CHRISTOPHER ||align="center" |PETE's SPIM-in-a-suitcase |
| − | |align="center" style="background:mediumseagreen;"|'''11: | + | |- |
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| + | |align="center" style="background:mediumseagreen;"|'''11:00''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''11:15''' | ||
|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"|11:15||align="center"|11:20||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"|11:20||align="center"|11:30||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;"|'''13:15''' | |align="center" style="background:mediumseagreen;"|'''13:15''' | ||
|align="center" style="background:mediumseagreen;"|'''LUNCH''' | |align="center" style="background:mediumseagreen;"|'''LUNCH''' | ||
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| − | |align="center"|13:15||align="center"|13: | + | |align="center"|13:15||align="center"|13:25||align="center"|SESSION 3|| align="center"|Planning your Imaging Experiment ||align="center" |DAVIDE||align="center" | + introduction to new user project questions |
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| − | |align="center"|13: | + | |align="center"|13:25||align="center"|13:35||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Alf Honigmann, STED-lab||align="center" |ALF<br>(JAN)|| align="center" | Q & A with Alf about his lab, STED, and cooperation possibilities |
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| − | |align="center"|13: | + | |align="center"|13:35||align="center"|13:55||align="center" |SESSION <br>Meet & Greet||align="center" | Meeting Benoit Lombardot, Leader Scientific Computing facility||align="center" |BENOIT<br>(JAN)|| align="center" | introduction to bioinformatics service and image processing facility |
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| + | |align="center"|13:55||align="center"|14:25||align="center"|SESSION 4a<br> Project discussion|| align="center"|One volunteer presents his/her imaging problem shortly and discuss it with the whole group ||align="center" |BioDIP TEAM <br>+ BENOIT||align="center" |NOTE: ask for volunteers already on Monday, than again on Wednesday | ||
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| + | |align="center" style="background:mediumseagreen;"|'''14:25''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''14:30''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''BREAK''' | ||
| + | |align="center" style="background:mediumseagreen;"|'''SHORT BREAK'''|| align="center" style="background:mediumseagreen;"|'''BREAK''' || align="center" style="background:mediumseagreen;" | | ||
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| − | |align="center"| | + | |align="center"|14:30||align="center"|15:00||align="center"|SESSION 4b<br> Project discussion|| align="center"|Second volunteer presents his/her imaging problem shortly and discuss it with the whole group ||align="center" |BioDIP TEAM <br>+ BENOIT||align="center" |NOTE: ask for volunteers already on Monday, than again on Wednesday |
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| − | |align="center"| | + | |align="center"|15:00||align="center"|16:00||align="center"|SESSION 6|| align="center"|Course evaluation ||align="center" |BioDIP TEAM||align="center" |Gummy bear bags and/or fruits<br>white board + marker |
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Latest revision as of 17:06, 20 October 2016
Contents |
[edit] PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course December 2016
[edit] Tentative Schedule
[edit] SETUP - Wed Nov 30th and Thu Dec 1st (Fri Dec 2nd TA course)
Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF hallway on Thu
Part of teaching microscopes where already set up before for the TA course
Setup of all needed course material in Galeria on Thu starting 11AM
Equipment needed
- microphone for Peter E. and team
- 10 tables (we need to order them early on - Davide will do; for Wed evening)
- Microscopes (6 teaching stations, 1 demo station, Peter's diffraction demo scope) (we will try to order another microscope body)
- cell culture microscope (normally with EM people; currently moved to cell culture room 4th floor south; Jan knows and will take care of getting it for the course)
- 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, Benzocain crystals
- microscope handout booklet for each teaching station
- First day handout for students
- Light torches
- Cameras and lab-tops for teaching stations
- Cleaning stations for each system containing: cover slips, slides, Qtips, water, 70% EtOH, lens cleaning tissue, EDTA, immersion oil, nail polish
- Waste and glass waste 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
[edit] DAY ONE - Mon 5th December
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 8:30 | 09:00 | FINAL PREP | Test everything works | BioDIP TEAM | |
| 9:00 | 9:38 | 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 four volunteers) |
| 9:38 | 10:30 | Session 1 Theory |
PRINCIPLES OF LIGHT MICROSCOPY Historical aspects Very basic components and principles (incl. refraction and resolution basics) |
PETER EVENNETT (BioDIP TEAM) | students shortly watch airy pattern from hole in mirror at the teaching microsopes (~10:04 - 10:10) |
| 10:30 | 10:45 | BREAK | BREAK | ||
| 10:45 | 11:25 | SESSION 1 Practice 3 groups, 12min Rotation (+3min for switching stations) Timer: SEBASTIAN |
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 DAVIDE |
*capillaries, oil * coin-in-cup, water, beaker for water * red/green laser pointer with holder stand, plastic refraction demo setup with protractor and water, laminated image of ice bear in water/air *water, glycerol, oil immersion objectives *refractometer |
| 11:25 | 12:15 | SESSION 1 Theory |
Introduction to lenses and objectives Numerical aperture Magnification |
PETER EVENNETT | cut objectives |
| 12:15 | 13:00 | LUNCH | LUNCH | ||
| 13:00 | 13:50 | SESSION 1 Practice 15min (!) Rotation Timer: SEBASTIAN |
Milky Glass Block demo Show and discuss microscope parts (upright and inverted) NA measurements |
JAN/DAVIDE 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 |
| 13:50 | 14:40 | SESSION 2 Theory |
Microscope illumination Conjugate planes Apertures |
PETER EVENNETT | |
| 14:40 | 14:55 | BREAK | BREAK | ||
| 14:55 | 15:55 | SESSION 2 Practice (30min Rotation inlc. time for switching) Timer: SEBASTIAN |
conjugate planes on Peters microscope conjugate planes on optical bench + effect of changing field and aperture diaphragms on demo scope |
PETER EVENNETT JAN |
*Peters microscope setup *optical bench demonstrating a transmitted light microscope, incl. light source conjugate planes scheme hand outs |
| 15:55 | 16:05 | BREAK | BREAK | ||
| 16:05 | 16:30 | SESSION 3 Theory |
Koehler illumination (Microscope alignment) |
PETER EVENNETT | |
| 16:30 | 17:30 | SESSION 3 Practice |
Koehler illumination (Microscope alignment) |
BioDIP TEAM | students manual microscopes, screwdrivers, nice brightfield sample |
| 17:30 | 17:35 | BREAK | BREAK | ||
| 17:35 | 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" |
| 18:00 | 18:10 | SESSION 3 Theory |
Epi illumination | PETER EVENNETT |
[edit] DAY TWO - Tue 6th December
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 10:00 | Recap | day 1 | BioDIP TEAM | Questions teaching microscopes; conjugate planes schemes |
| 10:00 | 10:05 | BREAK | SHORT BREAK | ||
| 10:05 | 10:10 | Theory | Introduction to Peter Evennett's videos |
Jan | You tube videos |
| 10:10 | 10:50 | SESSION 1a DEMONSTRATION + THEORY |
Diffraction and Diffraction slide fun Diffraction string show Diffraction and Resolution |
PETER EVENNETT | diffraction slides, torch, "dashed" string, fabric, funny glasses if available: wave/ripple tank; interferometer |
| 10:50 | 11:05 | BREAK | COFFEE BREAK | ||
| 11:05 | 11:25 | SESSION 1a Practice Round Group rotation (10min each) |
Interference and Diffraction | DAVIDE BRITTA |
Mach-Zehnder interferometer demo setup Ripple tank with various accessories |
| 11:25 | 11:50 | SESSION 1b Demo and Theory |
ABBE's diffraction demonstration | BERT | Dan's ABBE Diffraction demo setup |
| 11:50 | 12:20 | SESSION 1b Practice |
Diffraction hands on on student microscopes | BioDIP TEAM | rulers as gratings, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm, some small scissors would be nice |
| 12:20 | 12:35 | SESSION 1c Theory |
Wrap - up & Q & A Diffraction |
PETER EVENNETT JAN |
|
| 12:35 | 13:15 | BREAK | LUNCH | ||
| 13:15 | 13:50 | SESSION 2 Theory and Demo |
Lens abERRations and corrections finite versus infinite tube length objective labeling/reading |
PETER EVENNETT JAN |
lenses with various sizes and shapes |
| 13:50 | 14:05 | SESSION 3 Theory |
Objective reading lateral vs angular magnification |
PETER EVENNETT JAN |
objectives, eyepieces, overhead projector with digital source switch |
| 14:05 | 14:10 | SESSION 2 Demo |
demo of spherical aberration | JAN | magnetic lens + laser suitcase on white board |
| 14:10 | 14:40 | SESSION 3 Practice Round 1 Group rotation (30min each) |
Cover glasses, sample mounting, Objective cleaning and infinity optics bench demo Objective reading |
JAN BRITTA |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter bench demo of infinity optics box with broken objectives + two 160 tube lens objectives cell culture microscope with finite tube length |
| 14:40 | 15:00 | BREAK | COFFEE BREAK | ||
| 15:00 | 15:30 | SESSION 3 Practice Round 2 Group rotation (30min each) |
Cover glasses, sample mounting, Objective cleaning and infinity optics bench demo Objective reading |
JAN BRITTA |
Coverglasses (High preciscion), different oils, slides, different cleaning reagents, cover glass thickness measure meter bench demo of infinity optics box with broken objectives + two 160 tube lens objectives cell culture microscope with finite tube length |
| 15:30 | 15:50 | SESSION 4 Theory |
Introduction to contrast | BERT | |
| 15:50 | 16:15 | 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 |
| 16:15 | 16:20 | BREAK | SHORT BREAK | ||
| 16:20 | 16:55 | SESSION 5b Practice |
Dark Field microscopy | BioDIP TEAM | diatom slides |
| 16:55 | 17:25 | SESSION 6a Theory |
Basics of Phase Contrast microscopy | DAVIDE | including videos from web and own |
| 17:25 | 17:30 | SESSION 7 Demonstration |
Cheek cell prep | JAN | Q-tips, slides, cover slips, PBS, plastic pipette, nail polish |
| 17:30 | 18:00 | SESSION 6b 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 7th December
| 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 | 10:05 | BREAK | SHORT BREAK | BREAK | |
| 10:05 | 10:30 | SESSION 1 Demonstration |
Polarized light microscopy | SEBASTIAN JAN |
for students and Sebastian: calcite crystal blocks, polarizers, paper with black spot; overhead projector stone samples, gummy bears, plastic dishes, plastic rulers... |
| 10:30 | 11:10 | SESSION 1 Theory and Demo |
Polarized light microscopy | SEBASTIAN | Mach-Zehnder interferometer setup |
| 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 | Mach-Zehnder interferometer setup |
| 12:20 | 13:00 | SESSION 2 Practice |
Differential Interference Contrast (DIC) | BioDIP TEAM JAN |
DIC-objectives with respective Nomarski prisms; cheek cell samples, diatoms |
| 13:00 | 14:00 | BREAK | LUNCH | ||
| 14:00 | 14:05 | SESSION Meet & Greet |
Meeting Mark Bickle, Leader Technology development studio screening facility |
MARK (JAN) |
Q & A with Mark about his facility |
| 14:05 | 14:25 | Wrap-up compare methods |
Transmitted light contrasting techniques | BERT BioDIP TEAM |
first comparison than Quiz with various videos of the different techniques; remind students on Friday's project discussion round |
| 14:25 | 14:30 | QUESTION ROUND | questions to Peter Evennett | PETER EVENNETT JAN |
|
| 14:30 | 14:55 | SESSION 3 Theory |
Fundamental concepts of fluorescence | JAN | fluorescent liquids in bottles plus laser pointer (blue, green, red; need stronger red + green ones!) (in seminar room for darkness) |
| 14:55 | 15:35 | SESSION 4a Theory + Demo |
Introduction to fluorescence microscopes and light sources |
DAVIDE JAN |
• Light sources • Lamp houses |
| 15:35 | 15:50 | BREAK | COFFEE BREAK | BREAK | |
| 15:50 | 16:10 | SESSION 4b Theory |
Introduction to fluorescence microscopy Filters, spectra etc. |
DAVIDE JAN |
Spectra Filters Filter cubes |
| 16:10 | 16:35 | SESSION 4c Practice |
Filters | BioDIP TEAM | laminated sheets with grids for spectra drawing red, green, blue, black board markers EtOH spray bottles, tissue |
| 16:35 | 16:50 | SESSION 4d Theory and Demo |
Introduction to fluorescence microscopy Filters, spectra objective transmission curves |
DAVIDE | spectra viewer |
| 16:50 | 16:55 | BREAK | SHORT BREAK | BREAK | |
| 16:55 | 18:05 | SESSION 4e Practice |
Spectraviewer Aligment of Mercury arc lamps Fluorescence imaging at microscopes |
JAN BioDIP TEAM |
lamp house, screw driver laminated sheets with DAPI/FITC/TRITC Spectra red, green, blue, board markers EtOH spray bottles + tissue Fluorescent labeled samples (Convalaria) |
| 19:00 | open end | Dinner | with Peter | BioDIP TEAM | good mood, time |
[edit] DAY FOUR - Thu 8th December
| 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 |
| 10:00 | 10:15 | SESSION 1 Theory |
Fluorophores | HELLA | - | |
| 10:15 | 10:45 | SESSION 2 Theory |
Detectors | BRITTA | - | CCD chip paper weight Demo: CCD chip under stereo microscope example cameras showing different chip sizes |
| 10:45 | 11:10 | SESSION 2 Demo & Theory |
Detectors | BRITTA | bench show advacned detectors lecture |
RT spot with RGB slider and camera objective PC nice sample for binning (coffee cup) |
| 11:10 | 11:25 | SESSION 2 Practice |
Detectors "QE" show |
JAN | students count times of laser pointer blinking | blinking laser pointer |
| 11:25 | 11:40 | BREAK | BREAK | BREAK | BREAK | BREAK |
| 11:40 | 11:55 | SESSION 3a Theory |
Digital images | BERT | Nyquist-Shannon what is a pixel spatial calibration |
|
| 11:55 | 12:00 | SESSION 3a Demo |
Digital images | JAN | Nyquist-Shannon spatial calibration |
overhead projector sheets with different sized squares as example for dexel size gummi bears, Sesame seeds |
| 12:0 | 12:25 | SESSION 3a Practice |
calculating dexel/pixel size | BioDIP TEAM | practice calculating needed dexel size for given optical setup | calculator text with given optical setup (within Bert's presentation) |
| 12:25 | 12:35 | SESSION 3a Practice |
calculating dexel/pixel size | BERT | practice calculating needed dexel size for given optical setup | evaluation of the results from practical plus more calculation examples |
| 12:35 | 13:30 | BREAK | LUNCH | LUNCH | LUNCH | LUNCH |
| 13:30 | 13:35 | SESSION Meet & Greet |
Meeting Tobias Fürstenhaupt, Leader EM facility | Tobias (JAN) |
Q & A with Tobias about his facility and cooperation with LMF | - |
| 13:35 | 13:45 | SESSION 3b Theory |
Quantitative Imaging | BERT | digitization in space, time & intensity aliasing |
- |
| 13:45 | 15:10 | SESSION 4 Practice |
discussion and practice imaging with CCD/CMOS cameras on student microscopes | BioDIP TEAM | check out basic camera vocabulary discussing spec sheets of student microscope cameras spatial calibration with ruler and FIJI LUT, saturation, histogram etc |
camera spec sheets (in microscope handbook at each teaching scope) Hamamatsu camera comparison list (extra sheet) camera vocabulary checklist (in microscope handbook at each teaching scope) microscope ruler Fluorescence Sample slides (Kidney / Cells...) |
| 15:10 | 15:25 | BREAK | COFFEE BREAK | |||
| 15:25 | 15:30 | SESSION Meet & Greet |
Meeting Hella Hartmann, BioDIP Coordinator | HELLA (JAN) |
Q & A with Hella about BioDIP and cooperation between the participating facilities | BioDIP website |
| 15:30 | 15:43 | SESSION 5a Theory |
OPTICAL SECTIONING introduction widefield & deconvolution |
JAN | - | labtop |
| 15:43 | 15:53 | SESSION 6 Theory |
CHROMATIC ABERRATION | DAVIDE | ||
| 15:53 | 16:20 | SESSION 5b Theory & Demo |
OPTICAL SECTIONING Laser Scanning Confocal |
JAN | "confocal equipment": laser pointer, mirror, broken scanning mirror | |
| 16:20 | 16:40 | BREAK | BREAK | |||
| 16:40 | 17:15 | SESSION 5c Theory& Demo |
OPTICAL SECTIONING 2-Photon Microscopy |
SEBASTIAN JAN |
dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength | |
| 17:15 | 17:45 | SESSION 5d Theory |
OPTICAL SECTIONING Spinning Disc Confocal |
BRITTA JAN |
beer bottle from Plzen laminated sheets and copies of Nipkow's and Petran's patents | |
| 17:45 | 18:00 | SESSION 5d Demo |
OPTICAL SECTIONING Spinning Disc Confocal |
JAN | DAN's "spinning-disc-on-a-bench" |
[edit] DAY FIVE - Fri 9th December
| FROM | TO | ACTIVITY | TOPICS | Responsible person(s) | Materials needed |
| 9:00 | 10:05 | Recap | day 4 | BioDIP TEAM | Question sheets with the real case problem calculators, pens voting kit? |
| 10:05 | 10:10 | BREAK | BREAK | BREAK | |
| 10:10 | 10:25 | SESSION 1a Theory & Demo |
OPTICAL SECTIONING TIRF |
BRITTA | small glass cube with olive oil over milky water (use more oil than water!) plus Dan's blue laser pointer |
| 10:25 | 10:50 | SESSION 1b Theory & Demo |
OPTICAL SECTIONING SPIM |
DAVIDE | glass block with brain/scull and red light sheet laser from ZEISS |
| 10:50 | 11:00 | SESSION 1c Demo |
OPTICAL SECTIONING SPIM |
CHRISTOPHER | PETE's SPIM-in-a-suitcase |
| 11:00 | 11:15 | BREAK | BREAK | ||
| 11:15 | 11:20 | SESSION 1d Theory |
OPTICAL SECTIONING Apotome |
JAN | |
| 11:20 | 11:30 | SESSION 1e Theory |
OPTICAL SECTIONING final remarks |
JAN | |
| 11:30 | 12:05 | SESSION 2 Theory |
SUPER-RESOLUTION SIM STORM STED Airyscan Sample Preparation |
BERT | |
| 12:05 | 12:15 | DISCUSSION | preparation for Monday hands-on sessions | SEBASTIAN BioDIP team |
white board |
| 12:15 | 13:15 | LUNCH | LUNCH | LUNCH | |
| 13:15 | 13:25 | SESSION 3 | Planning your Imaging Experiment | DAVIDE | + introduction to new user project questions |
| 13:25 | 13:35 | SESSION Meet & Greet |
Meeting Alf Honigmann, STED-lab | ALF (JAN) |
Q & A with Alf about his lab, STED, and cooperation possibilities |
| 13:35 | 13:55 | SESSION Meet & Greet |
Meeting Benoit Lombardot, Leader Scientific Computing facility | BENOIT (JAN) |
introduction to bioinformatics service and image processing facility |
| 13:55 | 14:25 | SESSION 4a Project discussion |
One volunteer presents his/her imaging problem shortly and discuss it with the whole group | BioDIP TEAM + BENOIT |
NOTE: ask for volunteers already on Monday, than again on Wednesday |
| 14:25 | 14:30 | BREAK | SHORT BREAK | BREAK | |
| 14:30 | 15:00 | SESSION 4b Project discussion |
Second volunteer presents his/her imaging problem shortly and discuss it with the whole group | BioDIP TEAM + BENOIT |
NOTE: ask for volunteers already on Monday, than again on Wednesday |
| 15:00 | 16:00 | SESSION 6 | Course evaluation | BioDIP TEAM | Gummy bear bags and/or fruits white board + marker |
[edit] DAY SIX - optional - Mon 12th December 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 / SUPER-RESOLUTION | BioDIP team | MZ1, LZ2, CZ6, SD4, D4, H1, H2, W1 we need to decide which systems to use |
| 13:45 | 14:00 | Meeting students at switchboard |
OPTICAL SECTIONING / SUPER-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 / SUPER-RESOLUTION | BioDIP team | MZ1, LZ2, CZ6, SD4, D4, H1, H2, W1 |
| 15:30 | 16:00 | BREAK | COFFEE | KATJA | |
| 16:00 | 17:30 | SESSION II hands-on |
OPTICAL SECTIONING / SUPER-RESOLUTION | BioDIP TEAM | MZ1, LZ2, CZ6, SD4, H1, H2, W1 |
