ANAT2241 The Virtual Microscope: Difference between revisions

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In Histology, you are expected to study the features of histological preparations as virtual images, which were scanned from real stained sections, which were mounted on glass slides and listed in the Learning Activities.  In these classes you may encounter structures and terminology not defined in lectures.  You will need to read about these structures in your textbooks.
In Histology, you are expected to study the features of histological preparations as virtual images, which were scanned from real stained sections, which were mounted on glass slides and listed in the Learning Activities.  In these classes you may encounter structures and terminology not defined in lectures.  You will need to read about these structures in your textbooks.
 
==Learning Activity==
Read sections in your course manual on General Hints on Staining Procedures and Routine Staining Protocols.
 
[https://moodle.telt.unsw.edu.au/mod/book/view.php?id=789982&chapterid=100719 The Virtual Microscope]


==Introduction==
==Introduction==
Line 20: Line 25:
# Note the 2-D shapes in the section and the major tissue components present and try to determine the approximate 3-D shape of the whole organ from which the section was taken.  Is the section cut randomly through the organ?  Is there an obvious lumen in the section?
# Note the 2-D shapes in the section and the major tissue components present and try to determine the approximate 3-D shape of the whole organ from which the section was taken.  Is the section cut randomly through the organ?  Is there an obvious lumen in the section?


===Abbreviations===
* '''XS''' - cross section
* '''TS''' - transverse section
* '''LS''' - longitudinal section
* '''LM''' - light microscope or light micrograph
* '''EM''' - electron microscope, or electron micrograph
* '''2-D''' = 2-dimensional
* '''3-D''' = 3-dimensional
===Dimensions===
1mm = 10<sup>3</sup> micrometres (µm) = 10<sup>6</sup> nanometres (nm)
A micrometre is often called a "micron" (µm); 1µm = 10<sup>-6</sup>m
===Resolving Powers===
* Unaided eye - approx. 0.1 mm = 100µm
* Light microscope - approx. 0.1 µm = 100nm
* Electron microscope - approx. 1 nm
==What are Virtual Slides?==
High magnification scanned digital images of tissue sections on glass slides acquired using a x40 microscope lens.
Stored in a multi-resolution file format and viewed in a web browser window with software capacity to “click and drag” and “zoom in” on the image.
Simulates the examination of glass slides with a real microscope, but with the added benefits of always having optimal focus and contrast, with orientation maintained and avoiding section-to-section variability. 
Advantages
* '''Common tissue''' - allows all students to examine the same scanned tissue section.
* '''Annotation''' - can add your own labelled structures to help with revision.
** These annotations can be shared with others.
** Can see demonstrator annotations (if available).
* '''Access''' - can access images from any internet connected computer.
== Microscopy Methods ==
This Lab is an introduction to cell biology methods using microscopy. It includes a brief historic background and relevant modern technological advances. The focus is more on the application of these techniques in cell biology, rather than a comprehensive understanding of the physics and technology underlying the techniques.
: "'''''Diffraction inevitably limits the resolution of microscopy to around half the wavelength of light'''''" Ernst Abbe (1873, German physicist)
This rule has recently been bent, not broken.....
Also take the time to look at the [[#Textbook References|Textbook References]] and some of the [[Cell Biology Images]] on this Wiki. Later in the course we will be visiting the Confocal Microscope Facility, so spend some time reading about this technique.
[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.1729 MBoC Figure 9-8. Four types of light microscopy]
[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?&rid=mboc4.figgrp.1717 Figure 9-2.  Resolving power]
== Microscopy Timeline ==
* '''1665''' - Robert Hooke publishes Micrographia, a collection of biological micrographs.
* '''1674''' - Anton van Leeuwenhoek improved simple microscope for biological specimens.
* '''1833''' - Brown published a microscopic observation of orchids, describing the cell nucleus.
* '''1898''' - Golgi first saw and described the Golgi apparatus by staining cells with silver nitrate.
* '''1931''' - Ernst Ruska first transmission electron microscope, TEM).
* '''1934''' - Frits Zernike describes phase contrast microscopy.
* '''1957''' - Marvin Minsky patents principle of confocal imaging.
* '''1953''' - Frits Zernike receives the Nobel Prize in Physics for invention of the phase contrast microscope.
* '''1955''' - George Nomarski theoretical basis of Differential interference contrast microscopy.
* '''1981''' - Gerd Binnig and Heinrich Rohrer develop the [[#Scanning Tunneling Microscope (STM)|Scanning Tunneling Microscope (STM)]].
* '''1981''' - Daniel Axelrod develop [[#Total Internal Reflection Fluorescence Microscope (TIRFM)|Total Internal Reflection Fluorescence Microscope (TIRFM)]].
* '''1981''' - Allen and Inoué perfected video-enhanced-contrast light microscopy.
* '''1986''' - Ernst Ruska, Gerd Binnig and Heinrich Rohrer receive the Nobel Prize in Physics for invention of the electron microscope (ER) and scanning tunneling microscope (GB and HR).
* '''2000''' - Hell and collaborators develop [[#Stimulated Emission Depletion Microscopy (STED)|Stimulated Emission Depletion Microscopy (STED)]]
* '''2008''' - Freudiger and Wei Min develop Stimulated Raman Scattering Microscopy (SRS)
==Fixation==
Techniques for tissue and cell fixation.
# Fresh Frozen - [https://cellbiology.med.unsw.edu.au/cellbiology/index.php/Cryostat_Sectioning_Movie_1 Cryostat Sectioning Movie]
# Precipitation
# Aldehyde Cross-linked
[[Image:Inverted_Biological_Microscope.jpg|thumbnail|Inverted Biological Microscope]]
==Histology Stains==
This table includes many of the common histology stains. Note that depending upon the stain used the same tissue can appear quite different. Check the Slide information panel to see the original histological stain.
===Haematoxylin and Eosin===
One of the most common staining techniques in pathology and histology. Acronym "H and E" stain. (H&E, HE)
{|
|-
! width=400px|<font color=blue>Haematoxylin</font>
! width=400px|<font color=red>Eosin</font>
|-
|
* Stains nuclei blue to dark-blue.
* Stains the matrix of hyaline cartilage, myxomatous, and mucoid material pale blue.
* Stains myelin weakly but is not noticeable if combined with eosin stain.
* combined with [[Histology Stains#Orange G|Orange G]] (H & Or. G.) instead of eosin, specifically stains the granules of acidophilic cells of the adenohypophysis (anterior pituitary).
|
* Stains cytoplasm pink to red; red blood cells are also bright red.
* Common counterstain to hematoxylin.
* Stain intensity varies with the formula as well as the fixative.
|}
{{Common Stains table}}
===Artefacts===
* '''Chatter artefact''' - fine parallel lines (Virtual slide - tendon)
* '''Tissue cut''' - often a neat straight edge to tissue (where cut has been made) to allow the tissue to sit flat.
* '''Tissue fold''' - darker well demarcated line with apparent disruption of the tissue structure (Virtual slide - artery)
* '''Tissue tearing''' - irregular "tear" with apparent disruption of the tissue structure. Can be due to something intrinsic to the tissue that is hard.
* '''Shrinkage''' - clear white spaces due to fixatives dehydrating tissues.
* '''Uneven staining''' - Tissue has an "mottled" appearance that does not coincide with any tissue structure.
See also - {{#pmid:25364159}}
==Support Tutorial==
2018 -  Please note the Slide software has been updated and some of the original software descriptions below no longer apply.
[http://tv.unsw.edu.au/video/tutorial-2-using-the-virtual-microscope '''UNSWTV''' - Tutorial Using the Virtual Microscope]
This 15 minute video tutorial will take you through the organization and basic controls of the Virtual Microscope.
{| class="wikitable collapsible collapsed"
! Transcript - Virtual Slide Tutorial
|-
|
:'''Links:''' [http://tv.unsw.edu.au/video/tutorial-2-using-the-virtual-microscope '''UNSWTV''' Tutorial Using the Virtual Microscope] | [http://tv.unsw.edu.au UNSWTV]
The following text is an approximate transcript for the UNSWTV video tutorial "Using the Virtual Microscope"
|-
| Hi There
Welcome to the support tutorial for UNSW courses using "The Virtual Microscope".
In particular ANAT2241 Histology - Practical 1 An introduction to the virtual microscope.
This current tutorial does not go through practical class content but will help you both use and understand "The Virtual Microscope" controls.
Begin by following the H&S Information for correct ergonomic set up and use of class computers.
Have your practical manual ready with pens and pencils to make both notes and drawings as you work through the class materials. You may also choose to keep notes on your own computer as you work through the class.
If you are using the Virtual Microscope in a practical class computer you will be able to open your Virtual Microscope start page directly from the desktop menu.
For any other computer (as I am demonstrating) begin by opening the online course support page.
From the Practicals table select practical 1 "The Virtual Microscope"
If you are on your own computer or outside UNSW a log in message will appear
"To access the Virtual Slides from outside UNSW, please log in."
Click OK
The log in screen will appear.
Enter your student number and zpass.
The first time you log in, then the the default Virtual Slides welcome will open. You can then go through your course portal to each practical class.
Alternatively, now go back on your browser now and reselect practical 1 "The Virtual Microscope"
This time you should go directly to your practical page.
This current tutorial ail not go through practical class content but will introduce the "The Virtual Microscope" controls.
In practical classes, ensure you
Begin by taking an overview look at all the slides in your class.
You will need to allocate sufficient time to looking through all these slides during the practical class, unless the demonstrator advises otherwise.
You will also see from the whole slide thumbnail:
# the overall staining appearance and tissue structure. This is often close to the overall anatomy of that tissue.
# Any major tissue artefacts or processing modification of the tissue (breaks or cuts, shrinkage)
# Note the slide title and organ (often similar)
# Note the species (including age) and staining technique.
Note that the slide sequence will usually match that in your practical manual and may also be the order that they will be demonstrated. Other histological resources and materials outside virtual slides may also be used in your classes.
The practical class demonstrator may discuss all slides as thumbnails before opening the first class slide.
Lets now open a slide to see the basic layout and controls of the Virtual Microscope.
Note - This tutorial will not discuss this tissue, only the controls used to change its viewing.
Click a slide thumbnail.
Please read note about Computer Requirements
A new browser page will open with the slide tissue visible in 2 windows.
All Virtual slides will have this same initial layout, but tissues may open at different initial magnifications.
# A larger lefthand main window which will be used to observe the tissue histology.
# A smaller righthand thumbnail window with a thumbnail view of the whole tissue under this are a series of controls and icons. This smaller window will be the focus of todays tutorial.
'''Larger lefthand window (main)'''
Always observe the whole section before making any changes to the magnification.
For your own reference purposes, it may be useful to either take a screenshot or drawing of this initial view and any useful future view. Screenshots can be imported into a number of programs that allow you to add your own annotations (labels, notes, arrows or boxes).
'''Smaller righthand window (thumbnail)'''
Under the thumbnail image are a number of image controls (contrast and magnification) initially visible, and a location control not visible.
===Contrast===
The black and white box relates to image contrast and the slider located beside it.
Dragging the black triangle to the left, decreases contrast. Making the image darker.
Dragging the black triangle to the right, increases contrast. Making the image lighter.
You can change the contrast on any virtual slide, the demonstrator will often suggest if this is required for optimal viewing.
===Magnification===
Under the contrast controls are 2 magnifying glass icons and a drop-down window with a number shown.
There are several ways of changing magnification, lets look at the magnifying glass icons first.
#  The "+" (green plus) icon increases magnification (zooms in).
#  The "-" (orange minus) icon deceases magnification (zooms out).
When you click the "+" (green plus) icon:
#  The lefthand main window will change magnification.
#  The righthand thumbnail window will highlight (yellow and black box) the region of the whole slide that is currently being viewed. This is useful to later identify your location within the whole tissue.
Now the drop-down window with a number shown.
When you click on this window the menu opens and a range of magnification values are now available to be selected. The overall magnification range may vary for different slides but the maximum available for any slide 40x, some only reaching 20x.
When a magnification is selected it will automatically zoom centred on the current view.
===Location===
The location of your view can be changed in both the main and thumbnail windows. This control is not immediately visible and requires you to "click and drag" over the image.
Main window - when you left click the mouse, a hand will appear and you can now drag the slide image to a different location. Note the righthand thumbnail yellow and black box will also change to match the viewed location.
Thumbnail window - when you left click the mouse, a arrows appear over the yellow and black box and you can now drag the slide image to a different location.
Note that by now using the magnification controls (+ or -) will remain centred over the current view location.
When finished with the slide, close this virtual slide window and the original practical class set will be available to select the next slide.
===Important note===
The demonstrator will be using the same virtual slides displayed on the class projectors and monitors.
Follow the demonstrators descriptions closely (they know the material).
# Initially by watching the displays and the associated description.
# If this is not easy or clear, by noting the demonstrators thumbnail image position and magnification to find the same region on your own computer's virtual slide.
# Do not immediately zoom to the highest magnification (unless directed to) but gradually zoom in to note tissue structure and relationships.
# If you get lost in the tissue, zoom back out and start again.
# If you miss a specific point or description, ask a tutor in the break between slides. Do not interrupt the demonstrator's presentation unless they have suggested that you can ask questions.
This ends the second help tutorial, using the virtual microscope.
thank you.
--[[User:Z8600021|Mark Hill]] 15:24, 21 February 2013 (EST)
|-
|
===Computer Requirements===
Flash Player will not function on any Apple iPad (iPad or mini-iPad). It can function on their laptop and desktop computers.
Virtual slides requires a Flash Player (Adobe) plug-in to be installed in the browser application and will not function without this player.
All practical class computers have this player installed.
If you are using your own desktop or laptop computer this plug-in may need to be installed before virtual slides will display. Ensure that you are downloading and installing the latest player and only from the official Adobe website.
|}
==Virtual Slides Computer Requirements==
* Virtual slides requires a Flash Player (Adobe) plug-in to be installed in the browser application and will not function without this player.
* '''Flash Player will not function on any Apple iPad''' (iPad or mini-iPad). It can function on their laptop and desktop computers.
** Note - all online practical support pages will display on any computer, tablet (including iPad) and mobile phone platform capable of running a web browser.
* All practical class computers have this player installed.
* If you are using your own desktop or laptop computer this plug-in may need to be installed before virtual slides will display.
* Ensure that you are downloading and installing the latest player version and only from the official Adobe website (http://get.adobe.com/flashplayer).
** Note - you should also be using the latest available browser software.
* If you install this plug-in yourself you may need to shutdown and restart the browser application before it will function.
==Electron Microscopy==
EM appearance and structure of: nucleus, nucleolus, nuclear envelope, nuclear pore, mitochondria, endoplasmic reticulum (smooth & rough), ribosomes, Golgi apparatus, lysosomes, microtubules, microfilaments, plasma (cell) membrane, microvilli, stereocilia, cilia, and junctional complexes.
{{Osmium}} used as the main staining technique for electron microscopy.
===Cilia===
{|
| [[File:Lung epithelium sem11.jpg|400px]]
| [[File:Lung_epithelium_cilia_em01.jpg|400px]]
|-
| Cilia and microvilli on respiratory epithelium. (scanning EM)
| Cilia cross-sections showing microtubules. (EM)
|}
===Junctional Complexes===
{|
| [[File:Epithelial junctions EM02.jpg|400px]]
A series of junctional complexes between adjacent epithelial cells.
|
* '''Tight junction''' - (zonula occludens), located nearest the lumen, extends from arrow 1 to arrow 2. The narrowing of the apparent intercellular "gap" (~90 A) is clearly visible, but the fusion line of the two apposed membranes cannot be clearly distin- guished at this magnification. Note that there is relatively little accumulation of dense cytoplasmic material along this part of the complex.
* '''Adherens junction''' - (zonula adhaerens)  intermediate junction extends from arrow 2 to arrow 3. A relatively wide intercellular space (~200 A) is maintained throughout the junction. Extensive condensation of cytoplasmic fibrils occurs as a fine feltwork along either side of the junction. This condensation is continuous with the terminal web (tw) into which the filamentous rootlets (r) of the microvilli penetrate. Plate-like densifications within the cytoplasmic feltwork can be seen along part of the junction, especially along the right side (pi).
* '''Desmosome''' - marked by arrows 4 and 5. This element is characterized by a wide intercellular space (~240 A) bisected by an intermediate line (id). Bundles of cytoplasmic fibrils (fd), coarser (diameter ~80 A) and more distinct than those of the terminal web, converge into dense plates (pd) on each side of the desmo- some. These plates are separated from the inner leaflets of the cell membrane by a zone of low density. Similar fibrils (if) appear throughout the remainder of the field below the terminal web.
|}
[[File:Desmosome 02.jpg|400px]] [[File:Desmosome_01.jpg|300px]]
Desmosome




{{ANAT2241 footer}}
{{ANAT2241 footer}}

Latest revision as of 18:30, 12 April 2018

ANAT2241 course banner.jpg

ANAT2241 This practical support page content is not part of the virtual science practical class and provides additional information for student self-directed learning purposes. All practical class pages are located on Moodle - ANAT2241

General Objective

An introduction to the use of the virtual microscope.

Specific Objective and Learning Activities

To learn the correct use of virtual microscopy using computers and to employ various virtual histological databases for enhancing learning as well as for revision purposes.


In Histology, you are expected to study the features of histological preparations as virtual images, which were scanned from real stained sections, which were mounted on glass slides and listed in the Learning Activities. In these classes you may encounter structures and terminology not defined in lectures. You will need to read about these structures in your textbooks.

Learning Activity

Read sections in your course manual on General Hints on Staining Procedures and Routine Staining Protocols.

The Virtual Microscope

Introduction

Histological sections, which are slices of tissue usually from 5 - 8µm thick (see Dimensions below), can be examined efficiently as follows:

  1. Use the Slide Catalogue in your course handbook to determine:
    1. The animal from which the section is taken.
    2. The stains used (thereby defining the colours of the major tissue components). Note that stains are not examinable.
  2. Low power sketches or notes made may help you to remember the main histological features of a section, e.g., which major tissue components are present.
  3. Note the 2-D shapes in the section and the major tissue components present and try to determine the approximate 3-D shape of the whole organ from which the section was taken. Is the section cut randomly through the organ? Is there an obvious lumen in the section?

Abbreviations

  • XS - cross section
  • TS - transverse section
  • LS - longitudinal section
  • LM - light microscope or light micrograph
  • EM - electron microscope, or electron micrograph
  • 2-D = 2-dimensional
  • 3-D = 3-dimensional

Dimensions

1mm = 103 micrometres (µm) = 106 nanometres (nm)

A micrometre is often called a "micron" (µm); 1µm = 10-6m

Resolving Powers

  • Unaided eye - approx. 0.1 mm = 100µm
  • Light microscope - approx. 0.1 µm = 100nm
  • Electron microscope - approx. 1 nm

What are Virtual Slides?

High magnification scanned digital images of tissue sections on glass slides acquired using a x40 microscope lens.

Stored in a multi-resolution file format and viewed in a web browser window with software capacity to “click and drag” and “zoom in” on the image.

Simulates the examination of glass slides with a real microscope, but with the added benefits of always having optimal focus and contrast, with orientation maintained and avoiding section-to-section variability.

Advantages

  • Common tissue - allows all students to examine the same scanned tissue section.
  • Annotation - can add your own labelled structures to help with revision.
    • These annotations can be shared with others.
    • Can see demonstrator annotations (if available).
  • Access - can access images from any internet connected computer.

Microscopy Methods

This Lab is an introduction to cell biology methods using microscopy. It includes a brief historic background and relevant modern technological advances. The focus is more on the application of these techniques in cell biology, rather than a comprehensive understanding of the physics and technology underlying the techniques.


"Diffraction inevitably limits the resolution of microscopy to around half the wavelength of light" Ernst Abbe (1873, German physicist)

This rule has recently been bent, not broken.....


Also take the time to look at the Textbook References and some of the Cell Biology Images on this Wiki. Later in the course we will be visiting the Confocal Microscope Facility, so spend some time reading about this technique.


MBoC Figure 9-8. Four types of light microscopy

Figure 9-2. Resolving power


Microscopy Timeline

  • 1665 - Robert Hooke publishes Micrographia, a collection of biological micrographs.
  • 1674 - Anton van Leeuwenhoek improved simple microscope for biological specimens.
  • 1833 - Brown published a microscopic observation of orchids, describing the cell nucleus.
  • 1898 - Golgi first saw and described the Golgi apparatus by staining cells with silver nitrate.
  • 1931 - Ernst Ruska first transmission electron microscope, TEM).
  • 1934 - Frits Zernike describes phase contrast microscopy.
  • 1957 - Marvin Minsky patents principle of confocal imaging.
  • 1953 - Frits Zernike receives the Nobel Prize in Physics for invention of the phase contrast microscope.
  • 1955 - George Nomarski theoretical basis of Differential interference contrast microscopy.
  • 1981 - Gerd Binnig and Heinrich Rohrer develop the Scanning Tunneling Microscope (STM).
  • 1981 - Daniel Axelrod develop Total Internal Reflection Fluorescence Microscope (TIRFM).
  • 1981 - Allen and Inoué perfected video-enhanced-contrast light microscopy.
  • 1986 - Ernst Ruska, Gerd Binnig and Heinrich Rohrer receive the Nobel Prize in Physics for invention of the electron microscope (ER) and scanning tunneling microscope (GB and HR).
  • 2000 - Hell and collaborators develop Stimulated Emission Depletion Microscopy (STED)
  • 2008 - Freudiger and Wei Min develop Stimulated Raman Scattering Microscopy (SRS)

Fixation

Techniques for tissue and cell fixation.

  1. Fresh Frozen - Cryostat Sectioning Movie
  2. Precipitation
  3. Aldehyde Cross-linked


File:Inverted Biological Microscope.jpg
Inverted Biological Microscope

Histology Stains

This table includes many of the common histology stains. Note that depending upon the stain used the same tissue can appear quite different. Check the Slide information panel to see the original histological stain.

Haematoxylin and Eosin

One of the most common staining techniques in pathology and histology. Acronym "H and E" stain. (H&E, HE)

Haematoxylin Eosin
  • Stains nuclei blue to dark-blue.
  • Stains the matrix of hyaline cartilage, myxomatous, and mucoid material pale blue.
  • Stains myelin weakly but is not noticeable if combined with eosin stain.
  • combined with Orange G (H & Or. G.) instead of eosin, specifically stains the granules of acidophilic cells of the adenohypophysis (anterior pituitary).
  • Stains cytoplasm pink to red; red blood cells are also bright red.
  • Common counterstain to hematoxylin.
  • Stain intensity varies with the formula as well as the fixative.
Histology Stains - Common Stains and Their Reactions
Stain
Nucleus
Cytoplasm
Collagen
RBCs
Other
Haematoxylin
blue
-
-
-
mucins - light blue
Eosin
-
pink
pale pink
bright red
colloid - pinkmuscle - red
Iron Haematoxylin
blue/black
-
-
-
Van Gieson
-
brown/yellow
red
yellow
muscle: yellow/browncartilage - pink
Verhoeff's Elastin
black
-
-
-
elastic fibres - black
Tartrazine
-
yellow
yellow
yellow
Silver Impregnation
-
-
grey/brown
-
reticular fibres - black
Methyl Green
dark green
light green
light green
green
Nuclear Fast Red
red
pink
pink
pink
Gomori's Trichrome
purple/red
purple
green
red
keratin - redmuscle - purple/red
Heidenhain's Azan
red
purple/red
deep blue
red
muscle - red
Osmium Tetroxide
-
-
brown
brown
myelin, lipids - black
Alcian Blue
-
-
-
-
mucins, - blue
Periodic acid-Schiff (PAS)
-
-
pink
-
mucins, glycogen, glycocalyx - magenta
Phosphotungstic Acid-Hematoxylin (PTAH)
blue
-
red
blue
muscle bands - blue
Masson's Trichrome
blue/black
red
green/blue
red
cartilage, mucins - blue or green; muscle - red
Luxol Fast Blue
-
-
-
variable
myelin - blue
Aldehyde Fuchsin
-
-
-
-
elastic fibres, mast cells - deep purple
Light Green
-
-
light green
-
Gallocyanin
dark blue
-
-
-
nucleic acids, Nissl granules - dark blue
Romanowsky (e.g. Leishman's)
blue
pink
acidophils - red, basophils - blue, azurophilic - purple
Aldehyde Pararosanilin elastic fibres - purple

Artefacts

  • Chatter artefact - fine parallel lines (Virtual slide - tendon)
  • Tissue cut - often a neat straight edge to tissue (where cut has been made) to allow the tissue to sit flat.
  • Tissue fold - darker well demarcated line with apparent disruption of the tissue structure (Virtual slide - artery)
  • Tissue tearing - irregular "tear" with apparent disruption of the tissue structure. Can be due to something intrinsic to the tissue that is hard.
  • Shrinkage - clear white spaces due to fixatives dehydrating tissues.
  • Uneven staining - Tissue has an "mottled" appearance that does not coincide with any tissue structure.


See also - Chatterjee S. (2014). Artefacts in histopathology. J Oral Maxillofac Pathol , 18, S111-6. PMID: 25364159 DOI.

Support Tutorial

2018 - Please note the Slide software has been updated and some of the original software descriptions below no longer apply.


UNSWTV - Tutorial Using the Virtual Microscope

This 15 minute video tutorial will take you through the organization and basic controls of the Virtual Microscope.


Virtual Slides Computer Requirements

  • Virtual slides requires a Flash Player (Adobe) plug-in to be installed in the browser application and will not function without this player.
  • Flash Player will not function on any Apple iPad (iPad or mini-iPad). It can function on their laptop and desktop computers.
    • Note - all online practical support pages will display on any computer, tablet (including iPad) and mobile phone platform capable of running a web browser.
  • All practical class computers have this player installed.
  • If you are using your own desktop or laptop computer this plug-in may need to be installed before virtual slides will display.
  • Ensure that you are downloading and installing the latest player version and only from the official Adobe website (http://get.adobe.com/flashplayer).
    • Note - you should also be using the latest available browser software.
  • If you install this plug-in yourself you may need to shutdown and restart the browser application before it will function.


Electron Microscopy

EM appearance and structure of: nucleus, nucleolus, nuclear envelope, nuclear pore, mitochondria, endoplasmic reticulum (smooth & rough), ribosomes, Golgi apparatus, lysosomes, microtubules, microfilaments, plasma (cell) membrane, microvilli, stereocilia, cilia, and junctional complexes.

(Stain - Osmium) used as the main staining technique for electron microscopy.

Cilia

Lung epithelium sem11.jpg Lung epithelium cilia em01.jpg
Cilia and microvilli on respiratory epithelium. (scanning EM) Cilia cross-sections showing microtubules. (EM)

Junctional Complexes

Epithelial junctions EM02.jpg

A series of junctional complexes between adjacent epithelial cells.

  • Tight junction - (zonula occludens), located nearest the lumen, extends from arrow 1 to arrow 2. The narrowing of the apparent intercellular "gap" (~90 A) is clearly visible, but the fusion line of the two apposed membranes cannot be clearly distin- guished at this magnification. Note that there is relatively little accumulation of dense cytoplasmic material along this part of the complex.
  • Adherens junction - (zonula adhaerens) intermediate junction extends from arrow 2 to arrow 3. A relatively wide intercellular space (~200 A) is maintained throughout the junction. Extensive condensation of cytoplasmic fibrils occurs as a fine feltwork along either side of the junction. This condensation is continuous with the terminal web (tw) into which the filamentous rootlets (r) of the microvilli penetrate. Plate-like densifications within the cytoplasmic feltwork can be seen along part of the junction, especially along the right side (pi).
  • Desmosome - marked by arrows 4 and 5. This element is characterized by a wide intercellular space (~240 A) bisected by an intermediate line (id). Bundles of cytoplasmic fibrils (fd), coarser (diameter ~80 A) and more distinct than those of the terminal web, converge into dense plates (pd) on each side of the desmo- some. These plates are separated from the inner leaflets of the cell membrane by a zone of low density. Similar fibrils (if) appear throughout the remainder of the field below the terminal web.

Desmosome 02.jpg Desmosome 01.jpg

Desmosome


Course Links

Moodle - ANAT2241 - 2019

Histology Glossary: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | ANAT2241 Support | Histology | Histology Stains | Embryology Glossary


Common Histology Stains  
Histology Stains - Common Stains and Their Reactions
Stain
Nucleus
Cytoplasm
Collagen
RBCs
Other
Haematoxylin
blue
-
-
-
mucins - light blue
Eosin
-
pink
pale pink
bright red
colloid - pinkmuscle - red
Iron Haematoxylin
blue/black
-
-
-
Van Gieson
-
brown/yellow
red
yellow
muscle: yellow/browncartilage - pink
Verhoeff's Elastin
black
-
-
-
elastic fibres - black
Tartrazine
-
yellow
yellow
yellow
Silver Impregnation
-
-
grey/brown
-
reticular fibres - black
Methyl Green
dark green
light green
light green
green
Nuclear Fast Red
red
pink
pink
pink
Gomori's Trichrome
purple/red
purple
green
red
keratin - redmuscle - purple/red
Heidenhain's Azan
red
purple/red
deep blue
red
muscle - red
Osmium Tetroxide
-
-
brown
brown
myelin, lipids - black
Alcian Blue
-
-
-
-
mucins, - blue
Periodic acid-Schiff (PAS)
-
-
pink
-
mucins, glycogen, glycocalyx - magenta
Phosphotungstic Acid-Hematoxylin (PTAH)
blue
-
red
blue
muscle bands - blue
Masson's Trichrome
blue/black
red
green/blue
red
cartilage, mucins - blue or green; muscle - red
Luxol Fast Blue
-
-
-
variable
myelin - blue
Aldehyde Fuchsin
-
-
-
-
elastic fibres, mast cells - deep purple
Light Green
-
-
light green
-
Gallocyanin
dark blue
-
-
-
nucleic acids, Nissl granules - dark blue
Romanowsky (e.g. Leishman's)
blue
pink
acidophils - red, basophils - blue, azurophilic - purple
Aldehyde Pararosanilin elastic fibres - purple
Haematoxylin and Eosin
One of the most common staining techniques in pathology and histology. Acronym "H and E" stain. (H&E, HE).


Haematoxylin
  • Stains nuclei blue to dark-blue.
  • Stains the matrix of hyaline cartilage, myxomatous, and mucoid material pale blue.
  • Stains myelin weakly but is not noticeable if combined with eosin stain.
  • combined with Orange G (H & Or. G.) instead of eosin, specifically stains the granules of acidophilic cells of the adenohypophysis (anterior pituitary).
Eosin
  • Stains cytoplasm pink to red; red blood cells are also bright red.
  • Common counterstain to hematoxylin.
  • Stain intensity varies with the formula as well as the fixative.

Practical Support

Pages can be accessed from any internet connected computer.

ANAT2241 Support Links: The Virtual Microscope | Covering and Lining Epithelia | Glandular Epithelia | CT Components | CT Types | Bone, Bone Formation and Joints | Muscle | Nervous | Blood | Eye | Cardiovascular | Respiratory | Integumentary | Gastrointestinal | Gastrointestinal Organs | Lymphatic and Immune | Endocrine | Urinary | Female Reproductive | Male Reproductive | Histology Stains | Histology Drawings | Practicals Health and Safety 2013 | Moodle - 2019


ANAT2241 This practical support page content is not part of the science practical class and provides only background information for student self-directed learning purposes.


Cite this page: Hill, M.A. (2024, March 28) Embryology ANAT2241 The Virtual Microscope. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/ANAT2241_The_Virtual_Microscope

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© Dr Mark Hill 2024, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G