Test-Teaching

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= Light Microscopy =
 
= Light Microscopy =
 +
== Principles of Light Microscopy ==
 +
The materials presented here contain basic information about the physics of light, the optics of lenses and the components of a microscope.
  
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Evennett_oct2008_01_principles-of-microscopy-part-1.pdf|Principles of Light Microscopy]]
 +
* [[media:Evennett_oct2008_02_lens-aberrations.pdf|Lens Aberrations ]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Microscopy_principles_guide-part-1.pdf|Basics of Microscopy (2008)]]
  
 +
== Illumination ==
 +
This section contains information about proper illumination of your sample in the microscope and details on one method termed "Köhler Illumination".
  
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Evennett_oct2008_01_principles-of-microscopy-part-2.pdf|Microscope Illumination]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Microscopy_principles_guide-part-2.pdf|Microscope Illumination (2008)]]
 +
* [[media:Ibarra_how-to-set-koehler-illumination.pdf|How to set Köhler Illumination (2008)]]
  
 +
== Theory of Image Formation ==
  
−
* [[media:Stereomicroscopes_notes.pdf|Stereomicroscopes]]
+
This section describes how the microscopical image is formed by diffraction and what consequences (like resolution) arise from that.
  
−
== Principles of light microscopy ==
+
'''Materials from the Peter Evennett Course'''<br>
−
* [[media:Microscopy_principles_guide.pdf|Basics of Microscopy (2008)]]
+
* [[media:Evennett_oct2008_03_diffraction.pdf|Diffraction and the Microscope Image]]
−
* [[media:Evennett_oct2008_01_principles-of-microscopy.pdf|Principles of Light Microscopy]]
+
 
−
* [[media:Evennett_oct2008_02_lens-aberrations.pdf|Lens Aberrations ]]
+
A video by Peter Evennett showing Abbes diffraction experiments can be found [[Peter_Evennett_-_Abbe_Diffraction_Experiments|here]] or on [http://vimeo.com/user795818/videos/sort:oldest Vimeo (in HD)].
−
== Koehler illumination ==
+
 
−
* [[media:Ibarra_how-to-set-koehler-illumination.pdf|Köhler Illumination (2008)]]
+
'''Materials from the BioDIP Course (2008)'''<br>
−
== Image Formation ==
+
* [[media:Contrasting techniques-1.pdf|Diffraction ]]
−
* [[media:Evennett_oct2008_03_diffraction.pdf|Diffraction ]]
+
 
−
== Contrast techniques for transmitted light microscopy==
+
== Contrast Techniques for Transmitted Light Microscopy==
−
* [[media:Contrasting_techniques.pdf|Diffraction, Resolution and Contrasting Techniques (2008)]]
+
Different techniques exist to enhance the contrast in your sample. In this section these contrasting techniques are described.
−
* [[media:Evennett_oct2008_04_contrast.pdf|Contrast]]
+
−
=== Dark field microscopy===
+
'''Materials from the Peter Evennett Course'''<br>
−
=== Phase contrast microscopy===
+
* [[media:Evennett oct2008 04 contrast-1.pdf|Contrast]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Contrasting_techniques-2.pdf|Contrasting Techniques]]
 +
=== Dark Field Microscopy===
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Evennett oct2008 04 contrast-2-dark-field.pdf|Dark Field Microscopy]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Contrasting_techniques-3-dark-field.pdf|Dark Field Microscopy]]
 +
=== Phase Contrast Microscopy===
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Evennett oct2008 04 contrast-3-phase-contrast.pdf|Phase Contrast Microscopy]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Contrasting_techniques-4-phase contrast.pdf|Phase Contrast Microscopy]]
 +
=== Polarized Light microscopy===
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Evennett_oct2008_05_polarised-light.pdf|Polarized Light Microscopy]]
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:Contrasting_techniques-5-polarized light.pdf|Polarized Light Microscopy]]
 
=== Differential Interference Contrast (DIC) microscopy===
 
=== Differential Interference Contrast (DIC) microscopy===
−
* [[media:Evennett_oct2008_06_interference-contrast.pdf|Interference Contrast]]
+
'''Materials from the Peter Evennett Course'''<br>
−
=== Polarized light microscopy===
+
* [[media:Evennett_oct2008_06_interference-contrast.pdf|DIC Microscopy]]
−
* [[media:Evennett_oct2008_05_polarised-light.pdf|Polarised Light]]
+
'''Materials from the BioDIP Course (2008)'''<br>
−
== Fluorescence microscopy ==
+
* [[media:Contrasting_techniques-6-DIC.pdf|DIC Microscopy]]
−
= Image Processing =
+
 
−
= Courses =
+
== Stereomicroscopy ==
−
== Peter Evennett Course ==
+
'''Peter Evennett Course'''<br>
 +
* [[media:Stereomicroscopes_notes.pdf|Stereomicroscopes]]
 +
'''BioDIP Course (2008)'''<br>
 +
 
 +
== Fluorescence Microscopy ==
 +
'''Peter Evennett Course'''<br>
 +
* [[media:Fluorescence_notes.pdf|Fluorescence Microscopy]]
 +
* [[media:Fluorescence_basics.pdf| Basics of fluorescence Microscopy]]
 +
'''BioDIP Course (2008)'''<br>
 +
* [[media:Fluorescence_Imaging.pdf|Fluorescence Imaging (2008)]]
 +
'''External Resources'''<br>
 +
* [[media:OpticalFilters_EssentialTools_08-12-09.pdf| Optical Filters - Essential Tools by Dr. Michael Sommerauer (AHF)]]
 +
* [[media:OpticalFilters_SpecifyingFilters_08-12-09.pdf| Optical Filters - Specifying Filters by Dr. Michael Sommerauer (AHF)]]
 +
 
 
= Advanced Microscopy =
 
= Advanced Microscopy =
 +
'''Materials from the Peter Evennett Course'''<br>
 +
* [[media:Confocal_notes.pdf|Confocal Microscopy]]
 +
* [[media:Optical_Sectioning_ProsAndCons10-2009.pdf|Optical Sectioning Methods - pros and cons (LMF)]]
 +
* [[media:DeconvolutionAndOpticalSectioning-prosandcons-11-2010.pdf|Deconvolution and Optical Sectioning - pros and cons-11-2010‎]]
 +
At [http://vimeo.com/user795818/videos/sort:oldest Vimeo(in HD)] we deposited some videos showing cool SPIM 3D reconstructions and the effects of the confocal pinhole etc.<br>
  
 +
'''Materials from the BioDIP Course (2008)'''<br>
 +
* [[media:CCD_intro_2008_oct.pdf|CCD Imaging (2008)]]
 +
* [[media:Digital_imaging_oct_2008.pdf|Digital Imaging (2008)]]
 +
* [[media:FRET.pdf|FRET by Mike Lorenz (2009)]]
 +
* [[media:FLIM.pdf|FLIM by Mike Lorenz (2009)]]
 +
* [[media:How_to_do_FRET.pdf|How to do FRET by Mike Lorenz (2009)]]
 +
* [[media:FLIM-FRET_data_examples.pdf|FLIM-FRET data examples by Mike Lorenz (2009)]]
  
 +
= Image Processing =
 +
 +
 +
== IPF Image Processing Courses ==
 +
* [[media:2011-10-Basics_of_Imaging_Processing_Course.pdf|What you need to know about Image Analysis - updated Oct 2011]]
 +
* [[media:QuantitativeColocAnalysis-10-2011.pdf‎|Quantitative Imaging for Colocalization Analysis (updated Oct 2011)]]
 +
* [[media:Intro-fiji-and-macros.pdf‎|Introduction to Fiji and Macro Programming (updated Jul 2011)]]
 +
* [[media:QuantitativeImagingPhDCourseFriday-10-2009.pdf| Quantitative Imaging and Image Processing/Analysis 10-2009 (IPF)]]
 +
* [[media:Quant_imag_and_image_processing1108.pdf|Quantitative Imaging and Basic Image Processing (2008)]]
 +
 +
* [http://fiji.sc/Category:Tutorials Fiji (is just ImageJ - batteries included) Tutorials]
 +
 +
==General Image Processing reading material==
 +
*[http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.php Image manipulation ethics - Tutorial - avoid twisted pixels], and the [http://www.springerlink.com/content/00311qw26613m261/fulltext.pdf original article]
 +
 +
==DIPP course from the TDS of the MPI-CBG==
 +
* [[media:Presentations_TDD_DIPP2011.zip|Presentations about multifactorial experimental design, automated microscopy and image analysis - updated Oct 2011]]
 +
 +
* [[media:Presentations_DIPP-course-TDS_2012_03.zip|Presentations about multifactorial experimental design, automated microscopy and image analysis - updated Mar 2012]]
 +
 +
== Matlab ==
 +
* [[media:Matlab-Fundamentals.pdf|Matlab Fundamentals - December 2010]]
 +
 +
See also the handouts of the [http://www.lmc.ethz.ch/Teaching/matlab_course Matlab for biologists] course at the Light Microscopy Centre of the ETH Z&uuml;rich and the [http://www.neural-circuits.org/teaching/programming-with-matlab materials] of the Matlab programming course for Biophysicists at Universidad Autónoma de Madrid.
 +
 +
= Courses =
 +
== Peter Evennett Course ==
 
Twice a year the BioDIP team together with Peter Evennett organizes a basic course about microscopy.  
 
Twice a year the BioDIP team together with Peter Evennett organizes a basic course about microscopy.  
  
Line 76: Line 160:
 
== Master Course ==
 
== Master Course ==
  
 +
= Other Resources =
  
−
== Cool Videos we made for teaching and information ==
 
−
[http://vimeo.com/user795818/videos/sort:oldest Videos at Vimeo (in HD)]
 
−
These show Abbe's diffraction experiments (Peter Evennett), cool SPIM 3D reconstructions, and the effects of the confocal pinhole etc.
 
−
 
−
 
−
=== BioDIP Microscopy Course ===
 
−
* [[media:Fluorescence_Imaging.pdf|Fluorescence Imaging (2008)]]
 
−
* [[media:CCD_intro_2008_oct.pdf|CCD Imaging (2008)]]
 
−
* [[media:Digital_imaging_oct_2008.pdf|Digital Imaging (2008)]]
 
−
* [[media:Quant_imag_and_image_processing1108.pdf|Quantitative Imaging and Basic Image Processing (2008)]]
 
−
* [[media:FRET.pdf|FRET by Mike Lorenz (2009)]]
 
−
* [[media:FLIM.pdf|FLIM by Mike Lorenz (2009)]]
 
−
* [[media:How_to_do_FRET.pdf|How to do FRET by Mike Lorenz (2009)]]
 
−
* [[media:FLIM-FRET_data_examples.pdf|FLIM-FRET data examples by Mike Lorenz (2009)]]
 
−
 
−
=== Peter Evennett Microscopy Course ===
 
−
 
−
* [[media:Fluorescence_notes.pdf|Fluorescence Microscopy]]
 
−
* [[media:Fluorescence_basics.pdf| Basics of fluorescence Microscopy]]
 
−
* [[media:Confocal_notes.pdf|Confocal Microscopy]]
 
−
* [[media:Optical_Sectioning_ProsAndCons10-2009.pdf|Optical Sectioning Methods - pros and cons (LMF)]]
 
−
* [[media:DeconvolutionAndOpticalSectioning-prosandcons-11-2010.pdf|Deconvolution and Optical Sectioning - pros and cons-11-2010‎]]
 
−
* [[media:QuantitativeImagingPhDCourseFriday-10-2009.pdf| Quantitative Imaging and Image Processing/Analysis 10-2009 (IPF)]]
 
−
 
−
==== add-on ====
 
−
* [[Peter_Evennett_-_Abbe_Diffraction_Experiments|video by Peter Evennett: Abbe's diffraction experiments]]
 
−
 
−
 
−
=== Companies' Resources ===
 
−
* [http://zeiss-campus.magnet.fsu.edu/index.html Zeiss Campus - Education in Microscopy and Digital Imaging - with flash tutorials]
 
−
* [http://www.olympusmicro.com/index.html Olympus Microscopy Resources]
 
−
* [http://www.microscopyu.com/tutorials/java/ Nikon's interactive Java tutorials and demonstrations for many light microscopy techniques]
 
−
* [[media:OpticalFilters_EssentialTools_08-12-09.pdf| Optical Filters - Essential Tools by Dr. Michael Sommerauer (AHF)]]
 
−
* [[media:OpticalFilters_SpecifyingFilters_08-12-09.pdf| Optical Filters - Specifying Filters by Dr. Michael Sommerauer (AHF)]]
 
−
 
−
=== Other Resources ===
 
−
* [http://micro.magnet.fsu.edu/primer/ Optical Microscopy Primer]
 
−
=== Related Sections ===
 
 
* [[Papers#Light_Microscopy|Papers]]
 
* [[Papers#Light_Microscopy|Papers]]
 
* [[Links#Microscopy_-_Infos_and_Introductions|Links]]
 
* [[Links#Microscopy_-_Infos_and_Introductions|Links]]
−
 
−
== Image Processing ==
 
−
=== IPF Image Processing Courses ===
 
−
* [[media:2011-10-Basics_of_Imaging_Processing_Course.pdf|What you need to know about Image Analysis - updated Oct 2011]]
 
−
* [[media:QuantitativeColocAnalysis-10-2011.pdf‎|Quantitative Imaging for Colocalization Analysis (updated Oct 2011)]]
 
−
* [[media:Intro-fiji-and-macros.pdf‎|Introduction to Fiji and Macro Programming (updated Jul 2011)]]
 
−
* [http://fiji.sc/Category:Tutorials Fiji (is just ImageJ - batteries included) Tutorials]
 
−
 
−
===General Image Processing reading material===
 
−
*[http://swehsc.pharmacy.arizona.edu/exppath/micro/digimage_ethics.php Image manipulation ethics - Tutorial - avoid twisted pixels], and the [http://www.springerlink.com/content/00311qw26613m261/fulltext.pdf original article]
 
−
 
−
==High Content Screening==
 
−
===DIPP course from the TDS of the MPI-CBG===
 
−
* [[media:Presentations_TDD_DIPP2011.zip|Presentations about multifactorial experimental design, automated microscopy and image analysis - updated Oct 2011]]
 
−
 
−
* [[media:Presentations_DIPP-course-TDS_2012_03.zip|Presentations about multifactorial experimental design, automated microscopy and image analysis - updated Mar 2012]]
 
−
 
−
== Other courses ==
 
−
=== Matlab ===
 
−
* [[media:Matlab-Fundamentals.pdf|Matlab Fundamentals - December 2010]]
 
−
 
−
See also the handouts of the [http://www.lmc.ethz.ch/Teaching/matlab_course Matlab for biologists] course at the Light Microscopy Centre of the ETH Z&uuml;rich and the [http://www.neural-circuits.org/teaching/programming-with-matlab materials] of the Matlab programming course for Biophysicists at Universidad Autónoma de Madrid.
 

Latest revision as of 17:37, 16 January 2014

delete gallery page and integrate it here

Contents

[edit] Light Microscopy

[edit] Principles of Light Microscopy

The materials presented here contain basic information about the physics of light, the optics of lenses and the components of a microscope.

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Illumination

This section contains information about proper illumination of your sample in the microscope and details on one method termed "Köhler Illumination".

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Theory of Image Formation

This section describes how the microscopical image is formed by diffraction and what consequences (like resolution) arise from that.

Materials from the Peter Evennett Course

A video by Peter Evennett showing Abbes diffraction experiments can be found here or on Vimeo (in HD).

Materials from the BioDIP Course (2008)

[edit] Contrast Techniques for Transmitted Light Microscopy

Different techniques exist to enhance the contrast in your sample. In this section these contrasting techniques are described.

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Dark Field Microscopy

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Phase Contrast Microscopy

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Polarized Light microscopy

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Differential Interference Contrast (DIC) microscopy

Materials from the Peter Evennett Course

Materials from the BioDIP Course (2008)

[edit] Stereomicroscopy

Peter Evennett Course

BioDIP Course (2008)

[edit] Fluorescence Microscopy

Peter Evennett Course

BioDIP Course (2008)

External Resources

[edit] Advanced Microscopy

Materials from the Peter Evennett Course

At Vimeo(in HD) we deposited some videos showing cool SPIM 3D reconstructions and the effects of the confocal pinhole etc.

Materials from the BioDIP Course (2008)

[edit] Image Processing

[edit] IPF Image Processing Courses

[edit] General Image Processing reading material

[edit] DIPP course from the TDS of the MPI-CBG

[edit] Matlab

See also the handouts of the Matlab for biologists course at the Light Microscopy Centre of the ETH Zürich and the materials of the Matlab programming course for Biophysicists at Universidad Autónoma de Madrid.

[edit] Courses

[edit] Peter Evennett Course

Twice a year the BioDIP team together with Peter Evennett organizes a basic course about microscopy.

[edit] Schedules/Content

[edit] Impression from the Peter Evennett course 2007

  • course announcement

  • Peter Evennett and Humberto at the optical bench

  • room overview - 2nd floor galeria

  • Peter at his demo microscope

  • it's all about lenses

  • Jan

  • the optical bench

  • Peter at the condenser

  • demonstration of refractive index with a cup, a coin and water

  • Peter Evennett

  • Peter & Peter, setting up the demo microscope

  • Tim Cross, finally at the pipette

[edit] Master Course

[edit] Other Resources

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