ANAT2241 The Virtual Microscope

From Embryology
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. 2017 Coordinator notice - Virtual slide links shown on these support pages are now transferred to the new Moodle links.

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


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?


  • 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


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, which 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. This allows all students to examine the same scanned tissue section.

Support Tutorial

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 (
    • 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.


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


Course Links

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

Virtual slides

Pages require student zpass to access.

The Virtual Microscope | Covering and Lining Epithelia | Glandular Epithelia | Connective Tissue Components | Connective Tissue Types | Blood | Bone, Bone Formation and Joints | Muscle Tissue | Nervous Tissue | Cardiovascular System | Respiratory System | Integumentary System (skin) | Gastro-Intestinal System I | Gastro-Intestinal System II | Liver, Gallbladder, and Pancreas | Lymphatic Tissue and Immune System | Endocrine System | Urinary System | Female Reproductive System | Male Reproductive System | Special Sense Organ: The Eye

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 | Blood | Bone, Bone Formation and Joints | Muscle | Nervous | Cardiovascular | Respiratory | Integumentary | GIT 1 | GIT 2 | GIT Organs | Lymphatic and Immune | Endocrine | Urinary | Female Reproductive | Male Reproductive | Eye | Histology Stains | Histology Drawings | Practicals Health and Safety 2013

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. 2017 Embryology ANAT2241 The Virtual Microscope. Retrieved October 23, 2017, from

What Links Here?
© Dr Mark Hill 2017, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G