Inclusions photography is very important for gemological documentation and scientific investigation; it allows gemologists from all over the world to share their observations and experience. On the other hand, spectacular photographs of the internal microworld of inclusions help to show its beauty to the general public and transforms photomicrography into a kind of creative artistic process.

In this page, we mention some of the aspects of photomicrography with no intention of comprehensive technical description of equipment and methods, just to share some experience and tricks used by the author.

Basically, to take a photograph of a very small object we need:

  • Photo camera
  • Magnification system
  • Illumination system


Additionally, some special accessories and techniques can be very useful, especially for inclusions photography, such as:

  • Immersion cell and liquids
  • Polarizing filters
  • Hardware and software for image stacking


All these photomicrography components are considered below. For more in-depth information please follow the links at the end of this page.


Photo camera and magnification system

Not so long ago, photography was totally different; you were not able to see the results of your shot until the film was processed in a photo lab, usually at least a couple of days after taking the picture. Digital photography has changed our life, making it much more graphic. Now most people carry smartphones with high resolution cameras in their pockets and can share images with the whole wide world in seconds.

Digital cameras also made photomicrography much easier and affordable. The possibility to see on the screen exactly the same picture that is instantly taken by the camera is a huge advantage in this field, in addition to the possibility of editing pictures digitally and close to zero cost of each shot in terms of materials.

Nowadays, there are a wide range of options of cameras that can be used for photomicrography, combined with some additional equipment. Photo of inclusions can be taken even with a smartphone camera, simply attaching a standard gemological 10x loupe to it, holding them together manually or by means of some accessories. Of course, you can’t change magnification and in general this technique has very limited possibilities, but it can work for a quick shot of something interesting when more sophisticated equipment is not available.

In the same way, even better images can be taken with a smartphone by simply changing the human eye by the camera to the front of the ocular of the microscope. In this case, all the magnification power of your gemological microscope and its different lighting systems can be used; the trouble is to find the correct distance from the ocular and hold the phone quite still during image capture.

To improve this simple technique, so called “digiscoping adapters” can be used to fix the smartphone or, even better, compact a digital camera in the correct position in front of a microscope’s ocular. This simple method can provide fast and decent inclusion pictures from a standard microscope without a special optical channel for fixed camera mounting.

Digiscoping adapter used with smartphone (left: Lozano Gemologos) and with compact digital camera (right: IGE)


Some microscopes are already designed with a photo camera incorporated inside the optical system. However, it is more common to use microscopes with a special optical channel for camera mounting outside. Such microscopes are called trinocular; in comparison to two binocular microscopes with only two channels for eyes. In this case, different cameras can be used with the same microscope, according to the necessities of the user.

Gemmological microscope BestScope with digital camera incorporated in microscope’s head. (IGE)


Different types of cameras can be mounted on trinocular microscopes, taking out the camera lens and using special adapters. In this case, the whole microscope is used as a camera lens. Not only special digital cameras for microscopes, but also standard reflex and modern mirrorless models can be used. The “live view” option is very convenient to see on the computer screen exactly the same picture that will be captured, much handier than an optical visor or small digital screen on the camera. This way the exact frame, focus and lighting can by directly adjusted before image capture.

Digital reflex cameras mounted on different trinocular microscopes.
Left: Nikon SMZ 10 (IGE), right: B&Crown head on Macrorail stage. 


B&Crown trinocular head on Macrorail stage, with digital reflex camera mounted and projecting images to the screen in Live View mode. The base of the microscope is used for transmitted light illumination.


Another simple possibility to get more magnification power from the standard camera lens is simply to locate it at a larger distance from the camera. Special rings are available for that purpose, with the possibility of combining them in a different manner to get the needed magnification. In this case, all lens adjustments such as diaphragm and zoom will be conserved. This method, however, will not allow magnifications as high as those obtained using microscope.

Finally, a magnification system can be constituted by a simple lens or microscope objective located at a large distance from the camera. To change magnification, the lens can be mounted on an adjustable accordion bellows attached to the camera. The advantage of this system is that the objective directly projects the image to the camera sensor, and a lot of microscope optics needed for observation simultaneous to photography are avoided. However, in this case the observation and object finding can only be done on the computer screen, and at high magnification that can be difficult.

Left: Camera with extension rings, accordion bellows and Shneider Componon lens, on Macrorail stage.
Right: Camera with accordion bellow and microscope objective. (


The solution can be an additional accessory for changing different objectives, to use less magnification objectives to find the object and then more potent ones for final shooting. Other disadvantages of this system in comparison to the trinocular microscope is its much reduced focal distance that makes appropriate lighting, use of immersion and other accessories needed for inclusions photography more difficult.

Camera with accordion bellows and exchangeable microscope objectives. (



There are four types of illumination commonly used in gemology; each one can be most suitable in some cases and not appropriate in others. These types are:

  • Transmitted light
  • Dark field illumination
  • Diffused episcopic light
  • Punctual directed light (fiber optic)


Transmitted light is very convenient for observation of inclusions and color distribution, but in many cases it can be difficult to use because pavilion facets reflect the light and impede correct illumination of the stone’s interior. This problem can be solved using immersion liquids, as explained below, or dark field illumination, consisting in oblique illumination of the stone from the lower part. In this case, light enters in the stone perpendicular to pavilion facets avoiding reflections, and all internal inclusions can be easily detected and observed, highlighted on the dark field located below.

Diffused episcopic illumination is especially useful for observation of external characteristics and polishing quality. Moving the stone and finding the position when its facets reflect light to the objective, gemologists can find scratches, polish lines, superficial graining, cavities and other external characteristics.

In addition, strong punctual directed light by means of a fiber optic illuminator is also widely used in gemology and photomicrography. It produces much stronger contrast than diffused light and some types of inclusions, like tiny exsolution rutile needles, can be only detected with this type of illumination. Fiber optic allows us to move the light source freely around the gem and play with subtle lighting angle changes for better photomicrographs.

Most common types of inclusions illumination. 1 – Module for dark field and bright field illumination; 2 – diffused episcopic illumination; 3 – fiber optic illuminator with dual light guides. (IGE)


Additional techniques of lighting can be used too, such as shadowing, UV lighting, differential interference contrast and others. They are described more in detail in the publications listed at the end of this page for additional reading.


Same fluid inclusion recorded in transmitted, episcopic and ultraviolet illumination. Multi-phase inclusion in quartz from Pakistan, with yellow petroleum, small amount of water in the lower right part, solid bitumen particles and vapor bubble. Field of view 7 mm.



To facilitate the pass of light through a faceted gemstone, immersion liquids are widely used in gemology. Liquid with high refractive index, close to that of the observed gem, will help to avoid light refraction on the stone-air border, facilitating the observation of the stone’s internal characteristics. This method is especially useful for color zoning observation, since it reveals true shapes and orientation of color zones, minimizing distortions caused by light refractions on the stone’s surface.

Natural sapphire observed in air and in methylene iodide immersion. Straight color zoning, typical for natural sapphires, is only visible in immersion.


Different immersion liquids are used in gemology. The choice of the liquid depends on refractive index of studied gem, trying to use the liquid with closest refractive index to the stone. Many of immersion liquids are toxic and/or inflammable and must be used with corresponding cautions. Some of commonly used immersion liquids are their refractive indexes (RI) are listed below:

  • Water, RI 1.33
  • Alcohol, RI 1.36
  • Glycerol, RI 1.47
  • Toluene, RI 1.50
  • Benzyl benzoate, RI 1.57
  • Bromoform, RI 1.595
  • Methylene iodide, RI 1.74


In the following example, the same faceted gem, natural chrysoberyl form Brazil, has been photographed in air and in two different immersion liquids. Note how the transparence of the gem is improving as liquid RI is going closer to the stone’s.

Same stone (natural Brazilian alexandrite, RI 1.67, 0.11 ct) observed in air (left) and in two different immersion liquids: alcohol (center) and toluene (right).


Different accessories can be used for observation of gems in immersion under microscope. In standard vertical setup, simple glass cell can be used, moving the stone with tweezers. However, it can be difficult to orient the stone to many angles of observation, and correct orientation of the sample may be crucial, especially for color zoning, as shown in the following example.  A special setup, called horizontal microscope or immerionscope, has been developed for this task.

The simplest way to observe a gemstone in immersion, using standard vertical microscope and glass cell and moving the stone with tweezers. (IGE)


Immerionscope Optika in Spanish Gemological Institute (IGE) gem testing laboratory.


Influence of orientation of the stone on the color zoning visibility. Natural Brazilian alexandrite (RI 1.67, 0.11 ct), toluene immersion. Left: casual orientation, uneven color distribution can be seen, but exact directions of color zoning are unclear. Center: one direction of color zoning is defined, while the other still unclear. Right: two directions of color zoning are defined, forming sharp angle corresponding to natural stone’s crystal faces.


For standard vertical setup microscopes, to allow better orientation of gems in immersion with possibility to rotate them in different directions, a special magnetic immersion cell has been proposed by Egor Gavrilenko and Anthony Cáceres. It is easy to manufacture, the complete explanation and pieces of the unit shown below can be downloaded here. Please remember that in this case the amount of immersion liquid is bigger than in a standard immersion cell, so additional cautions have to be taken working with inflammable and toxic liquids!


Magnetic immersion cell, by Egor Gavrilenko and Anthony Cáceres.


Immersion liquids also can be applied superficially on gems with rough or poorly polished surfaces to improve their transparence for inclusions observation. This technique, described by John Koivula as “quick polish”, offers an easy and nondestructive alternative to standard polishing and can be sufficient in many cases.

This sample of green artificial glass was submitted to IGE gem testing lab as a supposed natural rough peridot from Africa. In normal observation conditions its inclusions can’t be seen clearly because of a very irregular unpolished surface. In contrast, a drop of cedarwood oil on its surface provides a “quick polish” effect, so that spherical air bubbles can be clearly seen. Field of view 15 mm.


Polarizing filters

Most gems are optically anisotropic materials; they have double refraction property. When any object is observed through an anisotropic gem, it will be seen as a double image. The effect of double refraction is variable from one gem to another; it is strongly dependant on depth of inclusion and observation direction. In directions of a crystal’s optic axes and in gems crystallizing in a cubic system, double refraction is absent. However, for anisotropic gems, its effect can be very negative on image quality, causing less crispy or even doubled images.

To reduce the effect of double refraction, plane-polarizing filter can be placed between the gem and microscope objective. Rotating the filter, its best position can be found for inclusion observation and photography.

Plane-polarizing filter with additional adapter ring for mounting on microscope.


Same inclusion of dumortierite in quartz, without polarizing filter (left) and with polarizing filter (right).
Both images have no additional post-processing. Field of view 1 mm.


If one more plane-polarizing filter is placed below the stone, in position of polarization perpendicular to the upper one, a system of crossed polarizing filters will be created. In this position, optically isotropic inclusions can be detected and photographed. Also, anomalous double refraction can be observed, especially important for distingushing natural from synthetic HPHT grown diamonds.

A pair of crossed polars to use with microscope (left) and anomalous birefrigence in natural type Ia diamond (right, field of view 6 mm).


Image stacking

When a gemstone is observed under microscope, depending on the distance from the objective, there will be some focused objects and those that are too close or too far to be in focus. In photography, the depth of field (DOF) is the distance from the closest focused object to the farthest one. The DOF can be very variable for different optic systems and camera adjustments, but in general, when using a microscope, there will always be areas out of focus, and higher magnification corresponds to smaller DOF.

To avoid this problem, special post processing software products are widely used in photomicrography. They are based on the so called photo stacking technique, when instead of one shot a sequence of photographs is taken, with certain displacement of the camera or microscope head. The software analyses all the images of the sequence digitally and selects for the final image only the focused area to reconstruct the resulting image, focused in a complete area or at least on the object of interest. Some of the most advanced programs especially designed for image stacking are Helicon Focus, Zerene Z Stacker and Combine ZP.

Nice etching figures on Colombian emerald surface. Note the narrow focused zone in the middle part of the upper image (single shot) and completely focused image composed as a result of stacking of 12 shots (lower image). Field of view 6 mm.


Sequences of images for stacking can be taken manually, simply moving the camera or microscope head. But they are much better done using special automated devices, such as Macrorail stage, on which microscope head or photo camera with other magnification systems can be mounted.


Automated Macrorail stage, for camera or microscope head mounting.


Macrorail software makes all the procedure very straightforward, the same computer program controls the stage that moves the camera (or microscope head) and also the camera itself to take pictures at every step. After the sequence of images is taken, Macrorail software uses separately installed stacking programs for image processing within the same interface.

To know how many photographs should be taken, the depth of field of the optical system should be measured. For that, a simple trick can be used, by means of direct measurement of focused area on ruler, located under microscope, with known tilt angle, as shown below. A simple calculation provides DOF value, and it can be done for different magnifications of the microscope.

Ruler position and calculation of the Depth of Field (DOF) value. The width of the focused area (A) is measured as shown below. 


Observation and measurement of focused area width (‘A’ value in previous figure) for DOF calculation, for tilted ruler shown above.


One has to take also into account that for shooting inclusions inside minerals, DOF values will increase because the refractive index of the host mineral is higher than that of the air. To calculate DOF inside minerals, values of DOF measured in the air must be multiplied by host mineral’s refractive index. Also, if our optical system has zoom, DOF value should be calculated for different magnifications.

Example of calculation of the shots needed for different magnifications, in air and corrected for observation inside quartz (refractive index 1.55). An Excel worksheet is very handy for calculation of Macrorail software input data. Previously, DOF should be estimated as shown above.  The user only has to introduce the distance in air corresponding to the whole depth of stacking area and the refractive index of the host mineral to know how many shots have to be done.



Using software and hardware for image stacking.

Some gemologists criticize the use of stacking techniques for inclusions photomicrography, saying that artificially amplified depth of field produces unreal pictures, impossible to see under microscope and hence with less value for practical work. In our opinion, it is very powerful tool, but of course it should be used with good criterion, avoiding exaggerated and unreal-looking results. After all, when observing inclusions in practical gemological work we usually move the stone continuously, “scanning” the complete volume of gem with microscope’s focal plane and reconstructing 3D picture of inclusions in our brain, producing a result quite similar to what stacking software can provide. In contrast, in a static photograph we can’t visually follow the same inclusion in depth.

Maybe the use of image stacking can be compared to high dynamic range technique, which has also appeared thanks to the digital photography upswing and that also sometimes provides too unreal-looking results. However, if well used, it can greatly improve the images and make fantastic photographs in cases when it was simply impossible before.


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