PhD Course Nov 09

Latest revision as of 16:57, 19 November 2009

[edit] PhD Course Nov 09

[edit] Friday 13th Nov

Setup - all lmf staff move stuff to galleria Equipment needed

Microscopes
Optical bench
Spinning disk gadget
Polarazing sheets
Diffraction Grids
Fluorescent samples
Fluorescent Beads (Prepare slides)
First day Handout for students
Light torches

[edit] DAY ONE (Monday)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)
9:00	10:30	INTRODUCTION	GROUP PRESENTATION Wishes for the course The ideal microsocpe	LMF TEAM
		DEMO	Optical Bench	LMF TEAM
10:30	11:00	BREAK	BREAK	BREAK
11:00	12:30	LECTURE 1	Basics in Optics Characteristics of light Light sources Reflection, Absorption, Refraction Diffraction-Demo	Humberto
		Practical 1 (Group Rotation)	1) Capillary + oil and Coin in glass 2) Laser refraction + reflection 3) Different immersion objectives - Demo Tirf Obective + DV oil box	1) Pete 2) Silke 3) Britta
12:30	13:30	LUNCH	LUNCH	LUNCH
13:30	15:45	Lecture 2	Introduction to lenses Lens abberration Understanding Ray optics	Humberto
		Practical 2	Ray optics Drawing ray diagrams
		Practical 3 (Group Rotation)	1) Finding focal point of lenses + infinity + Colour fringes 2) Virtual and real images. 25cm distance 3) Image of Arrow in the microscope (upright and inverted)	1) Jan 2) Humberto 3) Pete + Britta
15:45	16:00	BREAK	BREAK	BREAK
16:00	17:00	Lecture 3	Microscope components Focusing, Field of View, Depth of field, depth of focus Planes (filament Demo) Conjugated planes Koehler illumination	Humberto
17:00	18:30	Practical 4	Glass cube demo and practise Focusing; Depth of field / focus Koehler illumination	LMF TEAM

[edit] DAY TWO (TUESDAY)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)
9:00	10:00	INTRODUCTION (groups of 3)	Koehler Exercise Questions	LMF TEAM
10:00	11:25	Practical 5	Diffraction grids / gratings
		LECTURE 4a	Diffraction The Eye Interference	Humberto
		Practical 6	Airy disk on the microscope through mirror	LMF TEAM
		LECTURE 4b	Resolution NA	Humberto
11:25	11:40	BREAK	BREAK	BREAK
11:40	12:40	Practical 7	1) NA Objectives - angle measurements 2) Diffraction Exercise on microscope 3) Fluorescent beads with variable NA	1) Silke 2) Dan 3) Britta
12:40	13:40	LUNCH	LUNCH	LUNCH
13:40	15:30	Lecture 5a	Contrasting techniques I Dark field	Humberto
		Practical 8a (4 groups)	Dark field	LMF TEAM
		Lecture 5b	Contrasting techniques I Phase contrast	Humberto
		Practical 8b (4 groups)	Phase contrast	LMF TEAM
15:30	15:45	BREAK	BREAK	BREAK
15:45	17:45	Lecture 6a	Contrasting techniques II Polarization	Humberto
		Practical 9a (4 groups)	Polarization	LMF TEAM
		Lecture 6b	Contrasting techniques II Differential Interference Contrast	Humberto
		Practical 9b (4 groups)	DIC	LMF TEAM

[edit] DAY THREE (Wednesday)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)
9:00	9:45	INTRODUCTION (groups of 3)	Questions	LMF TEAM
9:45	10:30	LECTURE 7	Objectives Objective correction Infinity optics	Humberto
10:30	10:45	BREAK	BREAK	BREAK
10:45	11:45	Practical 10	1) Lens Abberration 2) Objective reading and cleaning 3) Infinity optics on optical bench, coverslip thickness measurement	1) Humberto 2) Silke 3) Jan
11:45	12:30	LECTURE 8	Basics of Fluorescence Fluorochromes	Dan
12:30	13:30	LUNCH	LUNCH	LUNCH
13:30	15:00	LECTURE 9 (interactive)	Fluorescence Microscopy Filters	Silke
		Practical 11	Mercury lamp exchange and alignment Fluorescence imaging	LMF TEAM
15:00	15:45	Lecture 10	CCD	Britta
15:45	16:00	BREAK	BREAK	BREAK
16:00	16:45	Lecture 11	Digital Imaging	Dan
16:45	18:30	Practical 12 (4 groups)	Wide field systems + CCD	LMF TEAM

[edit] Checklist for Widefield/CCD practical

Exposure Time
- Gain
- Binning
- ROI
- Saturation
- Histogram
- Gamma
Mapping/LUTs
Images - Display
Scale - ruler
Pixel size

[edit] DAY FOUR (Thursday)

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)
9:00	9:30	INTRODUCTION (groups of 3)	Questions Filter reading	LMF TEAM
9:30	09:45		DEMO - CCD - Colour	Britta
9:45	10:15	LECTURE 12a	Optical sectioning	Dan
10:15	10:30	BREAK	BREAK	BREAK
10:30	11:45	LECTURE 12b	Confocal Microscopy Multiphoton microscopy Spinning disc TIRF	Dan
11:45	12:45	LUNCH	LUNCH	LUNCH
12:45	14:15	Practical 13a	SYSTEM ROTATION Leica confocal, Spinning disc, Delta Vision	Pete, Britta, Dan
14:15	14:30	BREAK	BREAK	BREAK
14:30	16:00	Practical 13b	SYSTEM ROTATION Leica confocal, Spinning disc, Delta Vision	Pete, Britta, Dan
16:00	17:00 / 16:15	BREAK	SEMINAR / BREAK	BREAK
17:00 / 16:15	18:30 / 17:45	Practical 13c	SYSTEM ROTATION Leica confocal, Spinning disc, Delta Vision	Pete, Britta, Dan

[edit] DAY Five (Friday)

Please bring your own laptop and preinstall Fiji!!!

FROM	TO	ACTIVITY	TOPICS	Responsible person(s)

9:00	10:00	INTRODUCTION (groups of 3)	Questions	LMF TEAM
10:00	11:30	LECTURE 13a	Digital Images What is image processing	Dan
		Practical 14	Fiji (... is just ImageJ)
11:30	11:45	BREAK	BREAK	BREAK
11:45	13:00	LECTURE 13b	Image processing	Dan
		Practical 14	Fiji (... is just ImageJ)
13:00	14:00	LUNCH	LUNCH	LUNCH
14:00	15:30		LMF booking database IFN concept, members and Wiki Final discussion	IFN
15:30	16:00		Evaluation	LMF TEAM

[edit] Office Duty

FROM	TO	MONDAY	TUESDAY	WEDNESDAY	THURSDAY	FRIDAY
Morning	first break	/	Britta	Dan	Pete	Britta
first break	lunch	Dan	Pete	Britta	Humberto	Silke
lunch	break	Silke	Silke	Pete	Humberto Silke	/
break	end	Pete	Dan	Humberto	Humberto Silke	/

PhD Course Nov 09

Latest revision as of 16:57, 19 November 2009

Contents

[edit] PhD Course Nov 09

[edit] Friday 13th Nov

[edit] DAY ONE (Monday)

[edit] DAY TWO (TUESDAY)

[edit] DAY THREE (Wednesday)

[edit] Checklist for Widefield/CCD practical

[edit] DAY FOUR (Thursday)

[edit] DAY Five (Friday)

[edit] Office Duty

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BioDIP wiki

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@@ Line 25: / Line 25: @@
 | align="center" style="background:#f0f0f0;width:140px"|'''Responsible person(s)'''
 |-
-| ||||||||
 |-
 | 9:00||10:30||align="center"|INTRODUCTION||align="center" | GROUP PRESENTATION <br> Wishes for the course <br> The ideal microsocpe||align="center" |LMF TEAM
@@ Line 57: / Line 56: @@
 |-
 |-
-| 13:30||15:30||align="center"|Lecture 2|| align="center" |Introduction to lenses <br> Lens abberration <br> Understanding Ray optics||align="center" |Humberto
+| 13:30||15:45||align="center"|Lecture 2|| align="center" |Introduction to lenses <br> Lens abberration <br> Understanding Ray optics||align="center" |Humberto
 |-
 |-
@@ Line 72: / Line 71: @@
 |-
 |-
-| style="background:DarkKhaki;"|'''15:30'''
+| style="background:DarkKhaki;"|'''15:45'''
-| style="background:DarkKhaki;"|'''15:50'''
+| style="background:DarkKhaki;"|'''16:00'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
 |-
 |-
-| 15:50||17:00||align="center"|Lecture 3|| align="center" |Microscope components <br> Focusing, Field of View, Depth of field, depth of focus <br> Planes (filament Demo) <br> Conjugated planes <br> Koehler illumination||align="center" |Humberto
+| 16:00||17:00||align="center"|Lecture 3|| align="center" |Microscope components <br> Focusing, Field of View, Depth of field, depth of focus <br> Planes (filament Demo) <br> Conjugated planes <br> Koehler illumination||align="center" |Humberto
 |-
 |-
@@ Line 99: / Line 98: @@
 | align="center" style="background:#f0f0f0;width:140px"|'''Responsible person(s)'''
 |-
-| ||||||||
 |-
 | 9:00||10:00||align="center"|INTRODUCTION <br> (groups of 3)||align="center" | Koehler Exercise <br> Questions||align="center" |LMF TEAM
 |-
 |-
-| 10:00||11:00||align="center"|LECTURE 4|| align="center" |The Eye <br> Numerical Aperture <br> Diffraction||align="center" |Humberto
+| 10:00||11:25||align="center" style="background:Moccasin;"|''Practical 5''
+|align="center" style="background:Moccasin;"|''Diffraction grids / gratings''||align="center" style="background:Moccasin;"|
 |-
 |-
 ||
 ||
-|align="center" style="background:Moccasin;"|''Practical 5''
+|align="center"|LECTURE 4a|| align="center" |Diffraction <br> The Eye <br> Interference||align="center" |Humberto
-|align="center" style="background:Moccasin;"|''Diffraction grids / gratings''||align="center" style="background:Moccasin;"|
 |-
 |-
@@ Line 116: / Line 114: @@
 ||
 |align="center" style="background:Moccasin;"|''Practical 6''
-|align="center" style="background:Moccasin;"|''Airy disk on the microscope on mirror''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|align="center" style="background:Moccasin;"|''Airy disk on the microscope through mirror''||align="center" style="background:Moccasin;"|''LMF TEAM''
 |-
 |-
-| style="background:DarkKhaki;"|'''11:00'''
+||
-| style="background:DarkKhaki;"|'''11:20'''
+||
+|align="center"|LECTURE 4b|| align="center" |Resolution <br> NA||align="center" |Humberto
+|-
+|-
+| style="background:DarkKhaki;"|'''11:25'''
+| style="background:DarkKhaki;"|'''11:40'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
 |-
 |-
-| style="background:Moccasin;"|''11:20''
+| style="background:Moccasin;"|''11:40''
 | style="background:Moccasin;"|''12:40''
 |align="center" style="background:Moccasin;"|''Practical 7''
-|align="left" style="background:Moccasin;"|''1) Apertures (Objectives and Condenser) - Cube <br> 2) NA Objectives - angle measurements <br> 3) Diffraction Exercise on microscope <br> 4) Fluorescent beads with variable NA''||align="left" style="background:Moccasin;"|1) Humberto <br> 2) Silke <br> 3) Dan <br> 4) Britta
+|align="left" style="background:Moccasin;"|''1) NA Objectives - angle measurements <br> 2) Diffraction Exercise on microscope <br> 3) Fluorescent beads with variable NA''||align="left" style="background:Moccasin;"|1) Silke <br> 2) Dan <br> 3) Britta
 |-
 |-
@@ Line 137: / Line 140: @@
 |-
 |-
-| 13:40||15:30||align="center"|Lecture 5|| align="center" |Contrasting techniques I <br> Dark field + Phase contrast||align="center" |Humberto
+| 13:40||15:30||align="center"|Lecture 5a|| align="center" |Contrasting techniques I <br> Dark field ||align="center" |Humberto
 |-
 |-
 ||
 ||
-|align="center" style="background:Moccasin;"|''Practical 8 <br> (4 groups)''
+|align="center" style="background:Moccasin;"|''Practical 8a <br> (4 groups)''
-|align="center" style="background:Moccasin;"|''Dark field and Phase contrast''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|align="center" style="background:Moccasin;"|''Dark field''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|-
+|-
+||
+||
+|align="center"|Lecture 5b|| align="center" |Contrasting techniques I <br> Phase contrast||align="center" |Humberto
+|-
+|-
+||
+||
+|align="center" style="background:Moccasin;"|''Practical 8b <br> (4 groups)''
+|align="center" style="background:Moccasin;"|''Phase contrast''||align="center" style="background:Moccasin;"|''LMF TEAM''
 |-
 |-
@@ Line 152: / Line 166: @@
 |-
 |-
-| 15:45||17:45||align="center"|Lecture 6|| align="center" |Contrasting techniques II <br> Polarization + DIC||align="center" |Humberto
+| 15:45||17:45||align="center"|Lecture 6a|| align="center" |Contrasting techniques II <br> Polarization||align="center" |Humberto
+|-
+|-
+||
+||
+|align="center" style="background:Moccasin;"|''Practical 9a <br> (4 groups)''
+|align="center" style="background:Moccasin;"|''Polarization''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|-
+|-
+||
+||
+|align="center"|Lecture 6b|| align="center" |Contrasting techniques II <br>Differential Interference Contrast||align="center" |Humberto
 |-
 |-
 ||
 ||
-|align="center" style="background:Moccasin;"|''Practical 9 <br> (4 groups)''
+|align="center" style="background:Moccasin;"|''Practical 9b <br> (4 groups)''
-|align="center" style="background:Moccasin;"|''Polarization foil <br> Polarization on microscope <br> DIC on microsocpe''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|align="center" style="background:Moccasin;"|''DIC''||align="center" style="background:Moccasin;"|''LMF TEAM''
 |-
 |}
@@ Line 173: / Line 198: @@
 | align="center" style="background:#f0f0f0;width:140px"|'''Responsible person(s)'''
 |-
-| ||||||||
 |-
 | 9:00||9:45||align="center"|INTRODUCTION <br> (groups of 3)||align="center" |Questions||align="center" |LMF TEAM
 |-
 |-
-| 9:45||10:45||align="center"|LECTURE 7|| align="center" |Objectives <br> Objective correction <br> Infinity optics||align="center" |Humberto
+| 9:45||10:30||align="center"|LECTURE 7|| align="center" |Objectives <br> Objective correction <br> Infinity optics||align="center" |Humberto
 |-
 |-
+| style="background:DarkKhaki;"|'''10:30'''
 | style="background:DarkKhaki;"|'''10:45'''
-| style="background:DarkKhaki;"|'''11:00'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
 |-
 |-
-| style="background:Moccasin;"|''11:00''
+| style="background:Moccasin;"|''10:45''
 | style="background:Moccasin;"|''11:45''
 |align="center" style="background:Moccasin;"|''Practical 10''
-|align="center" style="background:Moccasin;"|''1) Lens Abberration <br> 2) Objective reading and cleaning, coverslip thickness measurement <br> 3) Infinity optics on optical bench''||align="center" style="background:Moccasin;"|1) Humberto <br> 2) Silke <br> 3) Jan
+|align="center" style="background:Moccasin;"|''1) Lens Abberration <br> 2) Objective reading and cleaning <br> 3) Infinity optics on optical bench, coverslip thickness measurement''||align="center" style="background:Moccasin;"|1) Humberto <br> 2) Silke <br> 3) Jan
 |-
 |-
-| 11:45||12:15||align="center"|LECTURE 8|| align="center" |Basics of Fluorescence <br> Fluorochromes||align="center" |Dan
+| 11:45||12:30||align="center"|LECTURE 8|| align="center" |Basics of Fluorescence <br> Fluorochromes||align="center" |Dan
 |-
 |-
-| style="background:DarkKhaki;"|'''12:15'''
+| style="background:DarkKhaki;"|'''12:30'''
-| style="background:DarkKhaki;"|'''13:15'''
+| style="background:DarkKhaki;"|'''13:30'''
 |align="center" style="background:DarkKhaki;"|'''LUNCH'''
 |align="center" style="background:DarkKhaki;"|'''LUNCH'''||align="center" style="background:DarkKhaki;"|'''LUNCH'''
 |-
 |-
-| 13:15||15:00||align="center"|LECTURE 9 (interactive)|| align="center" |Fluorescence Microscopy <br> Filters||align="center" |Silke
+| 13:30||15:00||align="center"|LECTURE 9 (interactive)|| align="center" |Fluorescence Microscopy <br> Filters||align="center" |Silke
 |-
 |-
@@ Line 208: / Line 232: @@
 ||
 |align="center" style="background:Moccasin;"|''Practical 11''
-|align="center" style="background:Moccasin;"|''Fluorescence imaging''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|align="center" style="background:Moccasin;"|''Mercury lamp exchange and alignment <br> Fluorescence imaging''||align="center" style="background:Moccasin;"|''LMF TEAM''
 |-
 |-
@@ Line 227: / Line 251: @@
 | style="background:Moccasin;"|''18:30''
 |align="center" style="background:Moccasin;"|''Practical 12 (4 groups)''
-|align="center" style="background:Moccasin;"|''Mercury lamp exchange and alignment <br> Wide field systems + CCD''||align="center" style="background:Moccasin;"|''LMF TEAM''
+|align="center" style="background:Moccasin;"|''Wide field systems + CCD''||align="center" style="background:Moccasin;"|''LMF TEAM''
 |-
 |}
@@ Line 258: / Line 282: @@
 | align="center" style="background:#f0f0f0;width:140px"|'''Responsible person(s)'''
 |-
-| ||||||||
 |-
-| 9:00||9:45||align="center"|INTRODUCTION <br> (groups of 3)||align="center" |Questions <br> Filter reading||align="center" |LMF TEAM
+| 9:00||9:30||align="center"|INTRODUCTION <br> (groups of 3)||align="center" |Questions <br> Filter reading||align="center" |LMF TEAM
+|-
+|-
+| 9:30||09:45||||align="center"|DEMO - CCD - Colour||align="center" |Britta
 |-
 |-
@@ Line 272: / Line 298: @@
 |-
 |-
-| 10:30||12:00||align="center"|LECTURE 12b|| align="center" |Confocal Microscopy <br> Multiphoton microscopy <br> Spinning disc <br> TIRF <br> Project discussions||align="center" |Dan
+| 10:30||11:45||align="center"|LECTURE 12b|| align="center" |Confocal Microscopy <br> Multiphoton microscopy <br> Spinning disc <br> TIRF||align="center" |Dan
 |-
 |-
-| style="background:DarkKhaki;"|'''12:00'''
+| style="background:DarkKhaki;"|'''11:45'''
-| style="background:DarkKhaki;"|'''13:00'''
+| style="background:DarkKhaki;"|'''12:45'''
 |align="center" style="background:DarkKhaki;"|'''LUNCH'''
 |align="center" style="background:DarkKhaki;"|'''LUNCH'''||align="center" style="background:DarkKhaki;"|'''LUNCH'''
 |-
 |-
-| style="background:Moccasin;"|''13:00''
+| style="background:Moccasin;"|''12:45''
-| style="background:Moccasin;"|''14:30''
+| style="background:Moccasin;"|''14:15''
 |align="center" style="background:Moccasin;"|''Practical 13a''
 |align="center" style="background:Moccasin;"|''SYSTEM ROTATION <br> Leica confocal, Spinning disc, Delta Vision''||align="center" style="background:Moccasin;"|''Pete, Britta, Dan''
 |-
 |-
+| style="background:DarkKhaki;"|'''14:15'''
 | style="background:DarkKhaki;"|'''14:30'''
-| style="background:DarkKhaki;"|'''14:45'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
 |-
 |-
-| style="background:Moccasin;"|''14:45''
+| style="background:Moccasin;"|''14:30''
-| style="background:Moccasin;"|''16:15''
+| style="background:Moccasin;"|''16:00''
 |align="center" style="background:Moccasin;"|''Practical 13b''
 |align="center" style="background:Moccasin;"|''SYSTEM ROTATION <br> Leica confocal, Spinning disc, Delta Vision''||align="center" style="background:Moccasin;"|''Pete, Britta, Dan''
 |-
 |-
-| style="background:DarkKhaki;"|'''16:15'''
+| style="background:DarkKhaki;"|'''16:00'''
-| style="background:DarkKhaki;"|'''16:30'''
+| style="background:DarkKhaki;"|'''<font color = red> 17:00 / <font color = black> 16:15'''
 |align="center" style="background:DarkKhaki;"|'''BREAK'''
-|align="center" style="background:DarkKhaki;"|'''BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
+|align="center" style="background:DarkKhaki;"|'''<font color = red> SEMINAR / <font color = black> BREAK'''||align="center" style="background:DarkKhaki;"|'''BREAK'''
 |-
 |-
-| style="background:Moccasin;"|''16:30''
+| style="background:Moccasin;"|''<font color = red>17:00 / <font color = black>16:15''
-| style="background:Moccasin;"|''18:00''
+| style="background:Moccasin;"|''<font color = red>18:30 / <font color = black>17:45''
 |align="center" style="background:Moccasin;"|''Practical 13c''
 |align="center" style="background:Moccasin;"|''SYSTEM ROTATION <br> Leica confocal, Spinning disc, Delta Vision''||align="center" style="background:Moccasin;"|''Pete, Britta, Dan''