BasicsCoursePhDprog-PeterEvennett - schedule March 2014

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(→‎DAY THREE - Wed 19th March: removed DIC video)
(→‎DAY FIVE - Fri 21st March: final update)
 
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| align="center" style="background:#f0f0f0;"|'''Materials needed'''
 
| align="center" style="background:#f0f0f0;"|'''Materials needed'''
 
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| 9:00||10:05||align="center"|Recap ||align="center" |  day 3  ||align="center" |BioDIP TEAM ||align="center" |-||align="center" |Questions
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| 9:00||10:10||align="center"|Recap ||align="center" |  day 3  ||align="center" |BioDIP TEAM ||align="center" |-||align="center" |Questions<br>DIC video from web (9:05 - 9:10)
 
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| 10:05||10:50||align="center"|SESSION 1<br>Theory||align="center" | 2nd part Fluorescence Microscopy ||align="center" |DAVIDE<br>JAN||align="center" |- ||align="center" |Spectra <br>Filters <br>Filter cubes <br>  
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| 10:10||10:50||align="center"|SESSION 1<br>Theory||align="center" | 2nd part Fluorescence Microscopy ||align="center" |DAVIDE<br>JAN||align="center" |- ||align="center" |Spectra <br>Filters <br>Filter cubes <br>  
 
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|style="background:LemonChiffon;"|10:50
 
|style="background:LemonChiffon;"|10:50
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|style="background:LemonChiffon;"|11:00||align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice||align="center" style="background:LemonChiffon;"|Filters||align="center" style="background:LemonChiffon;"|BioDIP TEAM||align="center" style="background:LemonChiffon;"|-||align="center" style="background:LemonChiffon;"|  laminated sheets with grids for spectra drawing  <br>red, green, blue, black board markers<br>EtOH spray bottles, tissue  
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|style="background:LemonChiffon;"|11:05||align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice||align="center" style="background:LemonChiffon;"|Filters||align="center" style="background:LemonChiffon;"|BioDIP TEAM||align="center" style="background:LemonChiffon;"|-||align="center" style="background:LemonChiffon;"|  laminated sheets with grids for spectra drawing  <br>red, green, blue, black board markers<br>EtOH spray bottles, tissue  
 
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| style="background:mediumseagreen;"|'''11:00'''
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| style="background:mediumseagreen;"|'''11:05'''
 
| style="background:mediumseagreen;"|'''11:20'''
 
| style="background:mediumseagreen;"|'''11:20'''
 
|align="center" style="background:mediumseagreen;"|'''BREAK'''
 
|align="center" style="background:mediumseagreen;"|'''BREAK'''
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|-
 
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|style="background:LemonChiffon;"| 11:20
 
|style="background:LemonChiffon;"| 11:20
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|style="background:LemonChiffon;"| 12:15||align="center" style="background:LemonChiffon;"|SESSION 1<br>Practice|| align="center" style="background:LemonChiffon;"|Fluorescence imaging at microscopes|| align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"|- || 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 (Convallaria)
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|style="background:LemonChiffon;"| 12:20||align="center" style="background:LemonChiffon;"|SESSION 1<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;"|- || 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 (Convallaria)
 
|-
 
|-
 
|-
 
|-
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| 12:15||12:55||align="center"|SESSION 2<br>Theory|| align="center"|Detectors ||align="center" |BRITTA||align="center" |-||align="center" | CCD chip paper weight <br>example cameras showing different chip sizes <br> • RGB Slider Spot Camera setup <br> Demo: CCD chip under stereo microscope (for later)
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| 12:20||12:30||align="center"|SESSION 1<br>Theory|| align="center"|Chromatic Aberration Correction ||align="center" |DAVIDE||align="center" |-||align="center" |  
 
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| style="background:mediumseagreen;"|'''12:55'''
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| 12:30||13:15||align="center"|SESSION 2<br>Theory|| align="center"|Detectors ||align="center" |BRITTA||align="center" |-||align="center" | CCD chip paper weight <br>Demo: CCD chip under stereo microscope <br>example cameras showing different chip sizes
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| style="background:mediumseagreen;"|'''13:50'''
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|-
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| style="background:mediumseagreen;"|'''13:15'''
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| style="background:mediumseagreen;"|'''14:00'''
 
|align="center" style="background:mediumseagreen;"|'''BREAK'''
 
|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'''
 
|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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| 13:50 ||14:20||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 slider and camera objective<br> PC<br> nice sample for binning  
+
| 14:00 ||14:35||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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|style="background:LemonChiffon;"|14:20
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|style="background:LemonChiffon;"|14:35
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|style="background:LemonChiffon;"|14:25||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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|style="background:LemonChiffon;"|14:40||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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|-
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| 14:25 ||14:50||align="center"|SESSION 3a<br>Theory|| align="center"|Digital images ||align="center" |BERT||align="center" |Nyquist-Shannon<br>what is a pixel<br>spatial calibration||align="center" | -
+
| 14:40 ||15:10||align="center"|SESSION 3a<br>Theory & Demo|| align="center"|Digital images ||align="center" |BERT<br>JAN||align="center" |Nyquist-Shannon<br>what is a pixel<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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|style="background:LemonChiffon;"|14:50
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|style="background:LemonChiffon;"|15:10
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|style="background:LemonChiffon;"|15:05|| align="center" style="background:LemonChiffon;"|SESSION 3<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
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|style="background:LemonChiffon;"|15:35|| align="center" style="background:LemonChiffon;"|SESSION 3<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
 
|-
 
|-
 
|-
 
|-
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| 15:05||15:25||align="center"|SESSION 3b<br>Theory|| align="center"|Quantitative Imaging ||align="center" |BERT||align="center" |digitization in space, time & intensity<br>aliasing ||align="center" |-
+
| 15:35||15:50||align="center"|SESSION 3b<br>Theory|| align="center"|Quantitative Imaging ||align="center" |BERT||align="center" |digitization in space, time & intensity<br>aliasing ||align="center" |-
 
|-
 
|-
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| style="background:mediumseagreen;"|'''15:25'''
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| style="background:mediumseagreen;"|'''15:50'''
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| style="background:mediumseagreen;"|'''15:45'''
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| style="background:mediumseagreen;"|'''16:05'''
 
|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;"|'''BREAK'''|| style="background:mediumseagreen;"|'''    '''|| style="background:mediumseagreen;"|'''    '''|| style="background:mediumseagreen;"|'''    '''
 
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|style="background:LemonChiffon;"|15:45
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|style="background:LemonChiffon;"|16:05
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|style="background:LemonChiffon;"|16:55|| align="center" style="background:LemonChiffon;"|SESSION 4a+b<br>Practice|| align="center" style="background:LemonChiffon;"|camera discussion on student microscopes|| align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"|check out basic camera vocabulary<br> discussing spec sheets of student microscope cameras<br>spatial calibration with ruler and FIJI|| align="center" style="background:LemonChiffon;"|camera spec sheets<br>Hamamatsu camera comparison list <br>camera vocabulary checklist <br> microscope ruler
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|style="background:LemonChiffon;"|17:00|| align="center" style="background:LemonChiffon;"|SESSION 4a+b<br>Practice|| align="center" style="background:LemonChiffon;"|camera discussion on student microscopes|| align="center" style="background:LemonChiffon;"|BioDIP TEAM|| align="center" style="background:LemonChiffon;"|check out basic camera vocabulary<br> discussing spec sheets of student microscope cameras<br>spatial calibration with ruler and FIJI|| align="center" style="background:LemonChiffon;"|camera spec sheets<br>Hamamatsu camera comparison list <br>camera vocabulary checklist <br> microscope ruler
 
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|style="background:LemonChiffon;"|16:55
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|style="background:LemonChiffon;"|17:00
 
|style="background:LemonChiffon;"|18:00ish<br>open end|| align="center" style="background:LemonChiffon;"|SESSION 4c<br>Practice|| align="center" style="background:LemonChiffon;"|Imaging with CCD cameras using LMF systems|| align="center" style="background:LemonChiffon;"|JAN<br>DAN<br>BRITTA<br>BERT<br>DAVIDE|| align="center" style="background:LemonChiffon;"|to whole group: <br>BioDIP Wiki with pages for all systesms<br><br>at single stations:<br>camera spec sheet of respective cameras<br>LUT, saturation, histogram etc|| align="center" style="background:LemonChiffon;"|Microscopes: <br> pDV of OMX (DAN, 2 students)<br> N-Storm (BRITTA, 3 students)<br> Oly-TIRF (BERT, 3 students) <br> self-built-system (JAN, 3 students)<br> DVcore (DAVIDE, 3 students) <br>Fluorescence Sample slides (Kidney / Cells...)<br> camera spec sheets of respective camera
 
|style="background:LemonChiffon;"|18:00ish<br>open end|| align="center" style="background:LemonChiffon;"|SESSION 4c<br>Practice|| align="center" style="background:LemonChiffon;"|Imaging with CCD cameras using LMF systems|| align="center" style="background:LemonChiffon;"|JAN<br>DAN<br>BRITTA<br>BERT<br>DAVIDE|| align="center" style="background:LemonChiffon;"|to whole group: <br>BioDIP Wiki with pages for all systesms<br><br>at single stations:<br>camera spec sheet of respective cameras<br>LUT, saturation, histogram etc|| align="center" style="background:LemonChiffon;"|Microscopes: <br> pDV of OMX (DAN, 2 students)<br> N-Storm (BRITTA, 3 students)<br> Oly-TIRF (BERT, 3 students) <br> self-built-system (JAN, 3 students)<br> DVcore (DAVIDE, 3 students) <br>Fluorescence Sample slides (Kidney / Cells...)<br> camera spec sheets of respective camera
 
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|align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|  
 
|align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|'''BREAK'''||align="center" style="background:mediumseagreen;"|  
 
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|10:45||11:30||align="center"|SESSION 1b<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Laser Scanning Confocal<br>2PM ||align="center" |JAN<br>BRITTA ||align="center" |"confocal equipment": <br> laser pointer, mirror, broken scanning mirror <br> dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength
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|10:45||11:40||align="center"|SESSION 1b<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Laser Scanning Confocal<br>2PM ||align="center" |JAN<br>SEBASTIAN ||align="center" |"confocal equipment": <br> laser pointer, mirror, broken scanning mirror <br> dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength
 
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|11:30||12:15||align="center"|SESSION 1c<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Spinning disc confocal<br>TIRF<br>SPIM ||align="center" |BRITTA<br>JAN ||align="center" |DAN's "spinning-disc-on-a-bench"<br>small glass cube with olive oil over milky water plus<br>5mW blue laser pointer (CRTD)<br>glass block with brain/scull and red light sheet laser from ZEISS
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|11:40||12:25||align="center"|SESSION 1c<br>Theory & Demo||align="center" | OPTICAL SECTIONING<br>Spinning disc confocal<br>TIRF<br>SPIM ||align="center" |JAN<br>DAN<br>BRITTA ||align="center" |* DAN's "spinning-disc-on-a-bench"<br>* small glass cube with olive oil over milky water (use more oil than water!) plus Dan's blue laser pointer <br>* glass block with brain/scull and red light sheet laser from ZEISS
 
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|12:15||12:30||align="center"|SESSION 1c<br>Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |PETE ||align="center" |PETE's SPIM-in-a-suitcase (on a bench this time)<br>glass block with whole scull<br>PETE's light sheet laser from whicked laser
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|12:25||12:35||align="center"|SESSION 1c<br>Demo||align="center" | OPTICAL SECTIONING<br>SPIM ||align="center" |PETE ||align="center" |PETE's SPIM-in-a-suitcase  
 
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|12:30||12:40||align="center"|SESSION 1d<br>Theory||align="center" | OPTICAL SECTIONING<br>Apotome<br>final remarks ||align="center" |JAN ||align="center" |
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|12:35||12:45||align="center"|SESSION 1d<br>Theory||align="center" | OPTICAL SECTIONING<br>Apotome ||align="center" |JAN ||align="center" |
 
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|12:40||12:50||align="center"|SESSION 1e<br>Theory||align="center" | SUPER-RESOLUTION<br>SIM<br>STORM ||align="center" |BERT ||align="center" |
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| style="background:mediumseagreen;"|'''12:45'''
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| style="background:mediumseagreen;"|'''13:30'''
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| style="background:mediumseagreen;"|'''12:50'''
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| style="background:mediumseagreen;"|'''13:45'''
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|align="center" style="background:mediumseagreen;"|'''LUNCH'''
 
|align="center" style="background:mediumseagreen;"|'''LUNCH'''
 
|align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" style="background:mediumseagreen;"|Optional: LMF tour
 
|align="center" style="background:mediumseagreen;"|'''LUNCH'''|| align="center" style="background:mediumseagreen;"|'''LUNCH'''||align="center" style="background:mediumseagreen;"|Optional: LMF tour
 
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| 13:45||14:00||align="center"|SESSION 2|| align="center"|Planning your Imaging Experiment ||align="center" |DAVIDE||align="center" | + introduction to new user project questions
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|13:30||13:45||align="center"|SESSION 1e<br>Theory||align="center" | OPTICAL SECTIONING<br>final remarks ||align="center" |JAN ||align="center" |
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|13:45||14:10||align="center"|SESSION 1f<br>Theory||align="center" | SUPER-RESOLUTION<br>SIM<br>STORM ||align="center" |BERT ||align="center" |
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 +
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| 14:10||14:20||align="center"|SESSION 2|| align="center"|Planning your Imaging Experiment ||align="center" |DAVIDE||align="center" | + introduction to new user project questions
 
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| 14:00||15:00||align="center"|SESSION 3<br> Project discussion|| align="center"|Three volunteer users present their imaging problems shortly and discuss it with the whole group ||align="center" |BioDIP TEAM||align="center" |NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low
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| 14:20||15:00||align="center"|SESSION 3<br> Project discussion|| align="center"|Two volunteers present their imaging problems shortly and discuss it with the whole group ||align="center" |BioDIP TEAM||align="center" |NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low
 
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Latest revision as of 15:23, 21 March 2014

Contents

[edit] PhD Program: Basics of Light Microscopy - Peter Evennett / LMF - Course March 2014

[edit] SETUP - Thu 13th and Fri 14th March

Prepare day boxes and teaching stations (microscopes with cameras etc) on tables in LMF on Thu
Setup of all needed course material in Galeria on Fri starting 12PM

Equipment needed

  • Microscopes
  • Optical bench
  • Spinning disk gadget
  • Polarizing sheets
  • Diffraction Grids
  • Sample map for each teaching station with: diatomes, liver tissue, convolaria, Benzocain crystals
  • First day handout for students
  • Light torches
  • Cameras and labtops for teaching stations
  • Cleaning stations for each system containing: cover slips, slides, Qtips, water, 70% EtOH, lens cleaning tissue
  • Waste and glass waste for each table
  • Box with screw drivers, telescope, eye pieces, ruler, mirror slide, DIC objective and wollaston prism for each microscope
  • 2 polarization filters for each microscope
  • Box with red, green, blue, black board marker, pen, pencil, sharpener, ruler, calculator for each microscope

[edit] DAY ONE - Mon 17th March

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
8:30 09:00 FINAL PREP Test everything works BioDIP TEAM
9:00 9:35 INTRODUCTION COURSE INTRO
WHO is WHO? Round table		 BioDIP TEAM White board and pen
9:35 10:38 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 (~10:05 - 10:10)
10:38 10:50 BREAK BREAK
10:50 11:30 SESSION 1
Practice
3 groups, 10min Rotation
Sebastian watched time		 capillary/plastic (Huisken) in oil demo
Coin-in-cup demo
red, green, blue laser through milky water bath -
measure angles, calculate refraction;
show immersion objectives
measure refraction with modern refractometer		 JAN
BRITTA
DAVIDE 		*capillaries, oil
* coin-in-cup, water
* red/green laser pointer with holder stand, plastic refraction demo setup with protractor and milky water
*water, glycerol, oil immersion objectives
*refractometer
11:30 12:30 SESSION 1
Theory		 Introduction to lenses and ojectives
Numerical aperture
Magnification
 PETER EVENNETT cut objectives
12:30 13:15 LUNCH LUNCH
13:15 14:00 SESSION 1
Practice
15min (!) Rotation
Timer: Sebastian		 Milky Glass Block demo
Show and discuss microscope parts (upright and inverted)
NA measurements		 JAN
BRITTA
BERT 		*milky glass block, teaching microscope, coloured filters for microscope, iris objective
*slides with arrows, simple upright and inverted microscope
*horizontal protractor on stand, objective holder, 2 air objective with different (!) NAs (and maybe an iris objective), calculator, pencils, rubber
14:00 14:45 SESSION 2
Theory		 Microscope illumination
Conjugate planes
Apertures		 PETER EVENNETT
14:45 15:00 BREAK BREAK
15:00 16:05 SESSION 2
Practice
(30min Rotation)
Timer: Sebastian		 conjugate planes on Peters microscope
conjugate planes on optical bench		 PETER EVENNETT
JAN 		*Peters microscope setup
*optical bench demonstrating a transmitted light microscope, incl. light source
conjugate planes scheme hand outs
16:05 16:40 SESSION 3
Theory		 Koehler illumination
Epi illumination
(Microscope alignment)		 PETER EVENNETT
16:40 17:45 SESSION 3
Practice		 Koehler illumination
(Microscope alignment)		 BioDIP TEAM students manual microscopes, screwdrivers, nice brightfield sample
17:45 18:00 SESSION 4
Theory & Practice		 Eyepieces
Depth of field
Depth of focus		 PETER EVENNETT
BioDIP TEAM 		students microscopes with 10x/0.25 and 40x/0.65 objectives
Stereoscope with a "sample"

[edit] DAY TWO - Tue 18th March

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
9:00 10:10 Recap day 1 BioDIP TEAM Questions
teaching microscopes; conjugate planes schemes
10:10 11:00 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
11:00 11:20 BREAK COFFEE BREAK


11:20 11:50 SESSION 1b
Demo and Theory 		ABBE's diffraction demonstration BERT Dan's ABBE Diffraction demo setup
11:50 12:15 SESSION 1b
Practice		 Diffraction hands on on student microscopes BioDIP TEAM gratings, place holder for objective Nomarski prism, piece of card board, microscopes without condenser, closed field diaphragm
12:15 12:55 SESSION 1b
Demo and Theory 		Peter's Diffraction video (w/o parts on Dark field and Phase contrast!) JAN
(PETER EVENNETT) 		video
12:55 14:00 BREAK LUNCH
14:00 14:15 SESSION 1b
Theory 		Wrap - up & Q & A
Diffraction 		PETER EVENNETT
JAN
14:15 14:55 SESSION 2
Theory and Demo		 Lens abERRations and corrections
objective labeling/reading 		PETER EVENNETT
JAN		 lenses with various sizes and shapes
magnetic lens + laser suitcase on white board
(15:00 - 15:05)
15:05 15:10 SHORT BREAK FRESH AIR
15:10 15:35 SESSION 3
Theory		 Introduction to contrast PETER EVENNETT
15:35 15:55 BREAK COFFEE BREAK
15:58 16:08 SESSION 3a
Video		 Peter's Dark Field diffraction video part JAN
(PETER EVENNETT) 		video
16:08 16:15 SESSION 3a
Theory		 Dark Field microscopy PETER EVENNETT next time: bring reflection dark field condenser
16:15 16:45 SESSION 3a
Practice		 Dark Field microscopy BioDIP TEAM diatom slides; cells from Gaia
16:45 16:55 SESSION 3b
Video		 Peter's Phase contrast diffraction video part JAN
(PETER EVENNETT) 		video
16:55 17:05 SESSION 3b
Theory		 Basics of Phase Contrast microscopy PETER EVENNETT
17:05 17:15 SESSION 3b
Demonstration		 Cheek cell prep JAN Q-tips, slides, cover slips, PBS, plastic pipette, nail polish
17:15 18:00 SESSION 3b
Practice		 Phase Contrast microscopy BioDIP TEAM cheek cell samples

[edit] DAY THREE - Wed 19th March

FROM TO ACTIVITY TOPICS Responsible person(s) Materials needed
9:00 10:10 Recap day 2 BioDIP TEAM example you tube videos on dark field and phase contrast (9:05-9:10)
Questions, pair of sieves, torches, microscopes
10:10 10:45 SESSION 1
Theory		 Objective reading
lateral vs angular magnification		 PETER EVENNETT
JAN 		objectives, eyepieces, overhead projector
10:45 11:00 BREAK BREAK BREAK
11:00 12:15 SESSION 1
Practice
Group rotation		 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
12:15 12:55 SESSION 2
Theory		 Polarized light microscopy PETER EVENNETT for students and Peter: calcite crystal blocks, polarizers, paper with black spot;
overhead projector
12:55 13:55 BREAK LUNCH
13:55 14:40 SESSION 2
Practice		 Polarized light microscopy PETER EVENNETT
BioDIP TEAM		 overhead projector, hair, stone samples, benzocain crystals, rulers, gummy bears, plastic dishes, ...
14:40 15:05 SESSION 3
Theory		 Differential Interference Contrast (DIC) PETER EVENNETT
15:05 15:50 SESSION 3
Practice		 Differential Interference Contrast (DIC) BioDIP TEAM
JAN		 cheek cell samples, diatoms
15:50 16:05 BREAK BREAK BREAK
16:05 16:25 Question round Questions to Peter Evennett PETER EVENNETT
BioDIP TEAM
16:25 17:05 SESSION 3
Theory		 Fundamental concepts of fluorescence JAN
BRITTA		 fluorescent liquids in bottles plus laser pointer (blue, green, red)
17:05 18:00 SESSION 4
Theory		 Introduction to fluorescence microscopy
and light sources 		DAVIDE
JAN		 • Light sources
• Lamp houses

[edit] DAY FOUR - Thu 20th March

FROM TO ACTIVITY TOPICS Responsible person(s) DEMO Activities Materials needed
9:00 10:10 Recap day 3 BioDIP TEAM - Questions
DIC video from web (9:05 - 9:10)
10:10 10:50 SESSION 1
Theory		 2nd part Fluorescence Microscopy DAVIDE
JAN		 - Spectra
Filters
Filter cubes
10:50 11:05 SESSION 1
Practice		 Filters BioDIP TEAM - laminated sheets with grids for spectra drawing
red, green, blue, black board markers
EtOH spray bottles, tissue
11:05 11:20 BREAK BREAK BREAK BREAK BREAK
11:20 12:20 SESSION 1
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 (Convallaria)
12:20 12:30 SESSION 1
Theory		 Chromatic Aberration Correction DAVIDE -
12:30 13:15 SESSION 2
Theory		 Detectors BRITTA - CCD chip paper weight
Demo: CCD chip under stereo microscope
example cameras showing different chip sizes
13:15 14:00 BREAK LUNCH LUNCH LUNCH LUNCH
14:00 14:35 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)
14:35 14:40 SESSION 2
Practice		 Detectors
"QE" show 		JAN students count times of laser pointer blinking blinking laser pointer
14:40 15:10 SESSION 3a
Theory & Demo		 Digital images BERT
JAN		 Nyquist-Shannon
what is a pixel
spatial calibration		 overhead projector
sheets with different sized squares as example for dexel size
gummi bears, Sesame seeds
15:10 15:35 SESSION 3
Practice		 calculating dexel/pixel size BioDIP TEAM practice calculating needed dexel size for given optical setup calculator
text with given optical setup
15:35 15:50 SESSION 3b
Theory		 Quantitative Imaging BERT digitization in space, time & intensity
aliasing 		-
15:50 16:05 BREAK BREAK
16:05 17:00 SESSION 4a+b
Practice		 camera discussion on student microscopes BioDIP TEAM check out basic camera vocabulary
discussing spec sheets of student microscope cameras
spatial calibration with ruler and FIJI		 camera spec sheets
Hamamatsu camera comparison list
camera vocabulary checklist
microscope ruler
17:00 18:00ish
open end		 SESSION 4c
Practice		 Imaging with CCD cameras using LMF systems JAN
DAN
BRITTA
BERT
DAVIDE		 to whole group:
BioDIP Wiki with pages for all systesms

at single stations:
camera spec sheet of respective cameras
LUT, saturation, histogram etc		 Microscopes:
pDV of OMX (DAN, 2 students)
N-Storm (BRITTA, 3 students)
Oly-TIRF (BERT, 3 students)
self-built-system (JAN, 3 students)
DVcore (DAVIDE, 3 students)
Fluorescence Sample slides (Kidney / Cells...)
camera spec sheets of respective camera
19:00 open end Dinner with Peter BioDIP TEAM good mood, time

[edit] DAY FIVE - Fri 21st March

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
10:00 10:30 SESSION 1a
Theory 		OPTICAL SECTIONING
introduction
widefield & deconvolution
chromatic aberration & correction 		JAN labtop
10:30 10:45 BREAK BREAK BREAK
10:45 11:40 SESSION 1b
Theory & Demo		 OPTICAL SECTIONING
Laser Scanning Confocal
2PM 		JAN
SEBASTIAN 		"confocal equipment":
laser pointer, mirror, broken scanning mirror
dual laser pointer (blue, green, red) to demonstrate penetration of diff. wavelength
11:40 12:25 SESSION 1c
Theory & Demo		 OPTICAL SECTIONING
Spinning disc confocal
TIRF
SPIM 		JAN
DAN
BRITTA 		* DAN's "spinning-disc-on-a-bench"
* small glass cube with olive oil over milky water (use more oil than water!) plus Dan's blue laser pointer
* glass block with brain/scull and red light sheet laser from ZEISS
12:25 12:35 SESSION 1c
Demo		 OPTICAL SECTIONING
SPIM 		PETE PETE's SPIM-in-a-suitcase
12:35 12:45 SESSION 1d
Theory		 OPTICAL SECTIONING
Apotome 		JAN
12:45 13:30 LUNCH LUNCH LUNCH Optional: LMF tour
13:30 13:45 SESSION 1e
Theory		 OPTICAL SECTIONING
final remarks 		JAN
13:45 14:10 SESSION 1f
Theory		 SUPER-RESOLUTION
SIM
STORM 		BERT
14:10 14:20 SESSION 2 Planning your Imaging Experiment DAVIDE + introduction to new user project questions
14:20 15:00 SESSION 3
Project discussion		 Two volunteers present their imaging problems shortly and discuss it with the whole group BioDIP TEAM NOTE: did ask for volunteers already on Monday, than again on Wednesday; this time input from student group was rather low
15:00 16:00 SESSION 3 Course evaluation BioDIP TEAM Gummy bear bags (last time it was apples :-))
white board + marker
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