An introduction to minerals and rocks under the microscope
An introduction to minerals and rocks under the microscope

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An introduction to minerals and rocks under the microscope

2.3 Minerals and the polarising microscope

2.3.1 Introduction to the polarising microscope

The polarising microscope enables the examination of mineral grains and observation of the properties outlined in Section 2.2. A polarising microscope is very similar to an ordinary microscope except that it has two polarising filters and a rotating stage on which the sample is placed. Figure 34 illustrates a typical layout. Plane-polarised light is produced by passing white light through a polarising filter (the polariser) located beneath the rotating stage.

Figure 34 Schematic representation of the polarising microscope.

The plane-polarised light then passes through the sample, which is presented as a thin slice of rock, 30 µm thick, mounted on a glass slide - this is a thin section (Figure 35). A magnified image is produced using two sets of lenses: a lower, objective lens, and an upper, eyepiece lens. The magnification can be varied by changing the objective lens. The image is focused by moving the lens assembly up or down, using the focusing knob. It is usual to start by looking at a thin section using plane-polarised light and low magnification. After this, the second polarising filter, the analyser, can be inserted to view the specimen between crossed polars.

Figure 35 A typical thin section (true size).

In this course, the Virtual Microscope substitutes for the polarising microscope. You will have the opportunity to familiarise yourself with the features and functionality of the Virtual Microscope in Activity 2.1.

The process of creating virtual microscope slides for Earth science creates image files of roughly 1GB for each thin section specimen using a motorised XY stage on a Leica DM4000M microscope. Rotation movies are digitised using an in-house system motorised Leica DM RP microscope.

Activity 2.1 Introduction to the Virtual Microscope

You should allow about 1 hour for this activity, which introduces the Virtual Microscope.

Task 1

This activity introduces you to the interface and functionality of the Virtual Microscope.

During this course, you will be using the Virtual Microscope, a system for viewing and exploring microscope slides (thin sections) of rocks using a computer and an internet browser window. The Virtual Microscope reproduces, and in some cases extends, the capabilities of the real microscope.

Open the Virtual Microscope [Tip: hold Ctrl and click a link to open it in a new tab. (Hide tip)] and you should see a screen similar to the one shown in Figures 36 and 37. We will use the gabbro thin section to illustrate the Virtual Microscope, but this may not be the image that appears the first time you access the Virtual Microscope.

Figure 36 A view of the main screen of the Gabbro page in the Virtual Microscope.

The screen is divided into a main viewing window and several functional areas that provide the ability to pan around the thin section, change magnification and light transmission conditions, and allow measurement (Figure 36). Two circles lower down the screen (Figure 37) display rotating images for viewing in plane-polarised light (left-hand circle), and between crossed polars (right-hand circle). These will only be displayed when you click on one of the circles on the full specimen view.

Figure 37 A view of one of the rotatable views (View 2) for the Gabbro page in the Virtual Microscope.
  1. In the upper left-hand corner, the catalogue of specimens can be accessed via two drop-down menus. The upper menu allows you to access the collection of rock specimen thin sections. The lower menu contains a series of links to characteristic examples of particular minerals and to various diagnostic features to reinforce your learning and for reference during your Virtual Microscope studies.

    A useful feature of the Virtual Microscope is a 'Random' button (adjacent to the catalogue), which can be used for self-test and revision purposes. When clicked, a random rock thin section is presented - this might be igneous, metamorphic or sedimentary. There are two stages of working in random mode: clicking the 'Clue' button gives the description associated with the rock thin section, and clicking 'Reveal' gives the name as well.

  2. Clicking and scrolling down the upper menu allows you to select from the menu of grouped igneous, metamorphic and sedimentary rocks, a cleavage slice of gypsum, rocks associated with a mapping activity later in the course, or a series of 'unknown' thin sections. Select 'Gabbro' in the 'Igneous' grouping for this demonstration.

  3. Gabbro

    The main window shows the full thin section view when initially selected from the menu. In the middle of the field of view there is a small cross (traditionally called the 'cross hairs' because real hairs were used in early microscopes); this is used for locating features in the specimen (see point 5).

    Note that a small number of coloured, semi-transparent circles with crosses are visible. These are 'hot spot icons' that, when clicked, display rotatable images in the circles below the main viewing window.

    The image in the main window can be manipulated either by zooming in and out, or by panning around the specimen at selected magnifications. As the main image is zoomed or panned, the thumbnail image in the top right-hand corner shows the location of the main window as a red rectangle superimposed on the thumbnail image. The dimensions of the field of view of the main window are given in millimetres at the top right above the thumbnail image.

    The image can be moved in several different ways by:

    • clicking and dragging the image itself
    • using the arrows on the right below the viewing window (further explained in point 6)
    • clicking and dragging the red rectangle on the thumbnail image in the top right-hand corner
    • clicking and holding the arrow keys on the keyboard.

    The image magnification can be varied in various ways:

    • If you wish to zoom in to a specific point in the thin section, simply click on the required spot, which then becomes the new centre of the field of view at a higher magnification. Another click zooms in further.
    • Zooming in and out can also be achieved using the computer keyboard. Press the 'A' key to zoom in, and the 'Z' key to zoom out.
    • A set of screen controls on the right below the main viewing window contains all the zooming and panning functions. These are explained in point 6.
    • Finally, there is a set of fixed magnifications, similar to a series of fixed objective lenses in a real polarising microscope, that can be used to standardise magnifications for some activities; see point 8.

    A scale bar below the main view window on the left shows 1 millimetre.

  4. Click on the upper-left hot spot icon of the image shown in point 3 (one of the coloured circles containing crosses) and the window will display two circular images known as 'rotating views'. At this point, two high-resolution movies are loaded into the browser. The circles may be blank while this is happening, but will display the word LOADING in the centre of the view:

    • the view on the left is an area of the thin section displayed in plane-polarised light
    • the view on the right is the same area of the thin section displayed as it appears between crossed polars.

    The high-resolution movies may take several seconds to load, but take considerably longer over a slow internet link. The process of loading the images can be speeded up considerably by pre-loading the movies - see point 13 for instructions.

    These rotating views are used to demonstrate several of the key optical properties of minerals in the thin sections: in plane-polarised light (PPL) and between crossed polars (XP). They can also be used to measure angles and can be viewed either with a 360° scale surrounding the view like a real microscope stage, or with a simple numerical indicator. You can choose between these two views by clicking on the 'stage' tick box in the bottom right-hand corner of the view.

    The images in these views (i.e. PPL or XP) can be rotated to view changing colours (pleochroism or interference colours) and extinction by clicking and dragging either image using the mouse, or by clicking one of the circle arrows labelled 'rotate stage' located between the rotating views at the top.

    Some of the main features in each rotating view are indicated by labels that can be switched on and off using the 'labels' tick box at the bottom right-hand corner of the screen.

  5. The location of the cross hairs is constantly displayed below the viewing window as X and Y coordinates. The sample can be moved to a specific location by typing the X and Y coordinates into the boxes and clicking the 'Go' button or by pressing the return key on the keyboard. This useful feature allows locations of particular features to be specified and communicated between different users.

  6. Below the main viewing window on the right-hand side are a series of image manipulation controls. Click on the '+' to zoom in, and the '−' to zoom out. Click on the arrows to move the viewing window across the thin section in the direction indicated. The circle containing an arrow resets the window to the full thin section view. Above the controls, a magnification slide bar indicates the zoom level. The magnification slider can also be clicked (it will go black as the mouse passes over it) and dragged to the right and left to zoom in and out of the thin section.

    We recommend that you try all the ways of moving the thin section and changing its magnification, to see which are best for you.

  7. At the top right-hand side of the main window, a thumbnail image of the main window displays a red rectangle showing the location of the current field within the thin section as a whole.

  8. Fixed magnifications are required for some tasks, and can also be used to switch quickly between magnifications and compare grain sizes at the same magnification in different thin sections.

  9. Each thin section can be viewed in plane-polarised light and between crossed polars. Switch between the two views using the labelled buttons.

  10. To the lower right of the thin section view are two tick boxes labelled 'grid' and '10 mm graticule'. Two curved arrows rotate the graticule and grid to measure features in any orientation.

    When the '10 mm graticule' box is selected, a 10 mm graticule with 0.1 mm divisions is superimposed over the thin section view, allowing direct measurement of features anywhere in the thin section once the features are moved to the centre of the field of view.

    When the 'grid' box is selected, a grid that does not change in size with magnification is superimposed on the thin section view. The grid can be used to define an area for study at a particular magnification, and is especially useful to estimate proportions of different minerals in a view

  11. The colour of the cross hairs and scale bar can be changed by clicking on the 'overlay colour' tick box.

  12. To the left of the thin section view, a description of the rock and its locality are given for each thin section. Minerals and features that appear in blue are hyperlinks to examples in the thin section, many of which are shown in the rotating views.

    Click 'olivine' in the gabbro description and the thin section view changes to display olivine at an appropriate magnification.

  13. As mentioned in point 4, if the rotating views load very slowly, they can be speeded considerably by pre-loading the movies as follows:

    Click the 'pre-load files' button at the bottom left of the screen below the rotating view circles. Follow the on-screen instructions to pre-load movies. Pre-loading a small number of thin sections intended for study in any particular session is recommended, rather than loading all rotation movies, which may take several minutes.

    Questions 2.1.1 and 2.1.2 use the Virtual Microscope using a virtual gypsum cleavage slice ('Miscellaneous' group). You may wish to reflect on the similarities between the two ways of seeing the same phenomenon and additional things you can observe using the Virtual Microscope.

Question 2.1.1

Select the 'Gypsum cleavage slice' from the catalogue of the Virtual Microscope. The single rhomb-shaped crystal fills more of the field of view even at low magnification. By default the first view will be in plain polarised light. Now select the view between crossed polars. Ignoring the crystal for the moment, why is the field of view outside the boundaries of the crystal clear or transparent in plain polarised light but black when viewed between crossed polars ?


This view corresponds to observation of the gypsum slice between the two sheets of polarised material. (Remember that you learned about minerals and polarised light in Section 2.2.) In plain polarised light, the glass slide on which the gypsum slice is mounted is transparent; however, when viewed between two pieces of polarised material with their polarising directions at right angles, the background and the glass slide appear black. This is because the light is polarised in one direction by the first sheet of polarising material and that direction is blocked by the second, thus allowing no light to pass.

This cleavage fragment exhibits a wide range of interference colours, including low-order colours at the grain margins. This is because it is not a true thin section with a uniform 30 μm thickness, but a broken fragment with variable thickness presenting different path lengths to light passing through different parts of it.

Question 2.1.2

Now consider the crystal slice in the view between crossed polars for the single crystal of gypsum. Given that this is part of a single crystal of gypsum, can you explain the reason for the range of interference colours you observe?


This cleavage fragment exhibits a wide range of interference colours (including low-order colours at the grain margins on the left-hand side) that correspond with the colours in the Michelle Levy chart of interference colours in Section 2.2.5. This is because it is not a true thin section with a uniform 30 μm thickness, but a broken fragment of a crystal with variable thickness presenting different path lengths to light passing through different parts of it. At its thinnest points close to the edge, the crystal exhibits first-order interference colours, whereas the thicker areas in the centre of the crystal exhibit third and fourth order colours.

Question 2.1.3

Returning to the plane-polarised view, in the main window, click the red circle 'hot spot' to load the rotating views. Explain what you observe as you rotate this part of the gypsum slice in (a) plane-polarised light and (b) between crossed polars.

  • a.On rotation in plane-polarised light, the appearance of the gypsum crystal slice remains the same except for changing from slightly darker to lighter due to varying relief, rather than pleochroism; the darkness of the glass mount beyond the crystal slice also changes very slightly too.
  • b.On rotation between crossed polars, the interference colours remain the same, although the brightness varies: every 90°, the crystal slice becomes completely dark. Thus, the crystal slice goes dark four times per complete rotation. The glass slide visible beyond the edge of the crystal slice remains dark in all orientations, as glass is isotropic. When the gypsum cleavage slice is in extinction, you may observe dust on the section and at least one small fragment of gypsum in a different orientation that still shows low-order interference colours when the main crystal is in extinction. In fact, you may also notice that this fragment never goes into extinction because two crystals on top of each other are very unlikely to be completely aligned with the polarisers. One of the reasons that geologists use very thin slices of rock is to avoid this effect and to observe the optical properties of individual crystals in thin section.

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