of data collection outdated.
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● Use base or low ISO for minimal
fuzziness/noise. ISO value versus exposure time and f-stop is a three-way
trade-off, in which the exact best choice depends on the exact circumstances and
● Avoid vibrations during exposure
(passing tram, walking around near the tripod during long exposures, pressing
the trigger roughly, etc.) – delay the trigger with the automatic release, use
touch-screen release or remote shutter release.
● Aim for even lighting of the
specimen to avoid shadows, ideally identical in all photographs. This is
especially important for recesses and parts underneath the specimen.
● Consciously pick a place to
start the image set, so that you can form a mental picture of the camera
positions and judge if further images are required. Once you have taken the
first few images, zoom in on the camera LCD and check the focus and level of
● Avoid taking photos against the
light because detrimental light reflections on the specimen are possible. Do not
photograph into strong lights that can cause lens flare. Sometimes, when
photographing specimens in exhibitions, it is possible to block individual
lights or reflections by simply holding a finger or the entire hand in front of
the lens (Figure 3 C). Alternatively, get another person to help you by holding
up a piece of cardboard.
General rules: photoset
● Move the camera in relation to
the specimen (or vice versa) to create parallax; do not take panorama photos
(many photographs from one camera position). The latter can be acceptable but
even small motions of the camera can drastically improve the quality of
● Each point on the specimen must
be well visible and in focus on at least two images. Any point not visible
directly will not be included in the final model (line-of-sight rule). Take care
to point the camera into recesses.
● Take photographs with 40-60%
overlap as rule of thumb. Avoid near-identical photographs, including
photographs that differ only in long-axis rotation (i.e. portrait versus
● Overview photographs can be
supplemented by close-ups, but much overlap is required.
● Take more photographs than
necessary, because unsuitable photographs can later beexcluded from model
creation and replaced by others, and gaps can be closed.
Figure 3: Mounted skeleton of the
ceratopsian dinosaur Protoceratops andrewsi AMNH 6417 in the AMNH exhibit. A.
Photograph taken through the glass cage that contains the specimen, and bears
inscriptions on one side. For a normal photograph, the presence of the letters
would be considered inacceptable, but as can be seen in B., where the features
found by Agisoft Photoscan Pro (search target in this case was 10.000 points)
are displayed as dots, the image is well suited for photogrammetry. Grey dots
indicate specific features found for the alignment process, blue dots those used
for the alignment. The specimen is in focus and thus delivers good points,
whereas the type on the glass is out of focus and delivers no points. C.
Photograph showing masking of strong reflections on the glass by blocking them
with the photographer’s hand.
● ‘Even lighting’ is the key criterion: less light (especially in combination
with a tripod) but no spotlights can be better than more but uneven light;
fluorescent ceiling lights and white collection cabinets surrounding the
specimen (acting as reflectors) work surprisingly well!
● Diffuse lights if necessary
(e.g., diffuse the sun with translucent plastic sheets).
● Cardboard (easily bought
everywhere) or white t-shirts for background and as reflectors to lighten up
shadows on the opposite side and underneath. Aluminum foil can also work, but
beware of possible light reflexes. Use darker materials for dark specimens to
avoid too much contrast in the images.
● Potentially use LED lights (easily
transportable, too) from low angle to light up shadows.
● If light conditions are poor and
a tripod is not available or feasible (e.g., wall-mounted specimens can require
work on a ladder), the exposure time may be too long for sharp photographs.
Consider using higher ISO values. If all else fails, photography with the
camera’s internal flash can produce in-focus pictures. However, flash-based
photography will always produce strong shadows and overexposed highlights. It is
essential to avoid shadows and white-outs on a sufficient number of pictures of
each part of the specimen to allow photogrammetric calculation. Alternation of
the shooting angles is very important. Shadowed areas must later be removed from
the calculation in the photogrammetry software, which may require masking.
● Poor Focus – This is the most basic factor to adjust correctly. Focused parts
should ideally include all important parts of the image.
● Wrong f-stop causing poor Depth
of Field – Shooting at low f-stop as often happens with automatic camera
settings can cause a major part of your object to be out of focus. For the best
focus, a stop down between f/8 and f/16 is recommended; above these f- stop
values, diffraction sets in and reduces the overall sharpness, rather than
increasing it. Check on internet resources (i.e., www.DPReview.com) to find the
best f-stop for certain lenses.
● Too few images usually result in
bad alignment, and thus gaps and errors in the model.
● Too little overlap (as above).
● Too many images increase
calculation time for no gain. Worse, too many images can lead to artifacts by
grouped alignment creating two points where there should be only one. However,
it is advisable to take many photos and use only a selection for photogrammetry,
especially if the specimen is not at one’s disposal.
● Too much overlap, duplicate
photographs (as above).
● Highly compressed images contain
artifacts that create false features which will be tracked by the software. RAW
images or high-quality JPEG are recommended.
● Unintended motion of the
specimen can lead to alignment problems if background features are included in
● Movement/Motion blur –
Constantly spinning a specimen on a turntable while shooting in burst mode will
likely fail because the shutter speed of most cameras is too slow. Slow shutter
introduces blur in the direction of the moving object, lowering your effective
resolution. Heavy specimens should be positioned absolutely stable – this is
important if placed e.g. in a sandbed.
● Lens distortion – The level of
distortion in most normal lenses is no problem for modern photogrammetric
software. However, it is recommended to avoid fish eye lenses with high barrel
● Changes in lighting (doors
opening, the sun moving, clouds, partial shade under trees, etc.) can lead to
alignment problems and/or gaps in the model. If a texture is calculated it can
contain artifacts. Moving shadows can be tracked as false movements and also
affect textures. Static light gives more consistent results; if feasible, it is
recommended to wait for an overcast sky for outdoor photography.
● Strong shadows – Dark shadows
often do not work well for point detection because they suffer from excessive
noise. Furthermore, the resulting textures are likely far from realistic colors.
● Taking pictures into the
direction of a light source can cause reflections on smooth surfaces or lens
flare, so that no or erroneous points will be found. At worst, “phantom objects”
can be caused by lens flare.
● Under-or over exposure – A
significantly under- or overexposed photograph loses usable detail. Inconsistent
exposure causes light and dark patches on the model.
● Unequal exposure within image
set – If the exposure differs significantly between photographs it may be
impossible for the program to find corresponding features. Even if images align
well, the following steps may partly fail, so that the final surface has
artifacts and unrealistic texture colors.
● Transparent and shiny surfaces –
Gathering data from specimens behind display cases or shiny surfaces (i.g.,
caused by lacquer, liquids, or enamel) is tricky. Current software cannot
distinguish between white pixels on the object and the reflection of light, as
it assumes all surfaces are non- reflective and opaque. Reflections of
surroundings in showcases do not move consistently with the surface of the
object and the angle of the photo; they may cause “ghost images” or holes in the
model. Furthermore, glass surfaces may distort the objects.
● Repetitive features – Tracking
certain repetitive pattern, such as architectural elements in the background,
ripple marks on track surfaces or honeycombs, can cause the software to wrongly
detect different instances as corresponding features. Such a “jump” can result
in strange conglomerate models with parts of the model presented repeatedly at
● Featureless textures – Plain
surface textures, such as at blank walls or even dusty surfaces, make feature
identification difficult; the software may fail in rebuilding depth of the model,
or even at building a model at all.
● Very thin specimens – If the
resolution of your photos of thin specimens (such as vertebrate ribs or mollusk
shells) is not high enough, the software-generated point cloud does not contain
enough points to accurately reproduce the shape of your object. The points may
not be placed in the exact same place along the length of the thin object.
Because photogrammetry requires
parallax either the camera or the specimen must move between shots, or both.
Depending on the size of the specimen and its mobility, as well as the space
available, one of two main methods is usually adopted: the turntable method, or
the walk-around method. For the former the camera is usually stationary, ideally
on a tripod. For the latter, the specimen usually does not move and the camera
is moved around it, either hand-held or on a tripod. Both methods have their
specific advantages and demands. Only occasionally is it advantageous to move
both the specimen and the camera, for example when the turntable method is used
with a scale bar that cannot be placed on the turntable with the specimen.
Aside from choosing between the
methods the image acquisition process is influenced also by considerations
regarding the potential risk of failure of the in-program model creation.
Photography aimed at optimizing the work process for the one-chunk model
creation method described below results in images that, if the one-chunk method
fails, do not make full use of the superior image alignment capabilities of the
multi-chunk method. We therefore recommend reading the sections Alignment
methods for more than one set of images and Background – blank or
The turntable method: basic
The turntable method has the camera on a tripod, and a series of photographs is
taken of the specimen on a turntable that is rotated across a small angle
between shots. Figure 4 shows the typical process for photographing a specimen
on a turntable. The photograph series thus forms a perfect circle of camera
positions around the specimen, with the camera always aimed at the central
vertical axis of the turntable. In order to cover the surface of a specimen with
a complex geometry it is usually necessary to vary the height of the camera
position in relation to the specimen by repeating the process shown in Figure 4
with the camera at a different height, so that several concentric circles of
photographs are taken. Undercuts may require additional photographs, with the
camera pointed off the main vertical axis. These images are usually created not
by moving the camera, but by manually shifting the specimen on the turntable and
optimizing the position for each photograph. The underside of the specimen has
to be photographed by flipping it over, and sometimes more than two positions
are required to capture the full surface geometry. The biggest advantages of the
turntable method are the ability to control the lighting, photograph speedily,
with fixed camera settings, and the control one has over the background. The
non-turning background must be as devoid of features as possible or masked, so
that no points are detected on it. Masking is additional work and should thus be
avoided, but it can allow combining photograph series from different specimen
positions into one photogrammetric reconstructions without any need to adjust
partial models to each other (see one-chunk method below), delivering the
highest quality models for the least amount of fiddling and editing.
The biggest drawback of the
turntable method is, aside from the requirement of a featureless background,
that it requires the specimens to be mobile, and sturdy enough to be handled.
Additionally, even the sturdiest turntables have weight limits, so that very
large specimens like sauropod dinosaur sacra or elephant skulls are too heavy.
Figure 4: Video showing the basic
photography process for specimens that can be placed on a turntable.
Turntable method for small
mobile specimens - using a turntable
The basic process is shown in
Figure 4. Use a turntable for even lighting and speedy photography. Heavy-duty
turntables for TV screens cost less than US$30. You may also use a Lazy Susan,
even an office chair that spins might be sufficient for some objects. Cover the
turntable with a featureless cover (white/black cardboard) and mark its vertical
outer side at 5° intervals as a visual guide for the rotation between
photographs. If possible, lift the specimen away from the turntable by placing
it on glass/perspex supports so no points are detected on the turntable, as its
cover will be out of focus. Use white packing foam bits to stabilize objects
that do not rest well in desired position.
Take photos at a shallow angle (0-15° from horizontal) at ~5° to 10° intervals
by turning the turntable. Then, lift the camera higher on the tripod (30-60°);
repeat. Then, lift the camera high above the specimen and take a few photographs
(3 or 4) from ~70-80° up. The more complex the specimen's geometry, the more
photographs are necessary.
Turn the specimen over (180° if
possible, but smaller angles are sufficient if enough of the lateral surfaces is
captured in each set to combine the two, i.e. if there is good overlap). Repeat
photo procedure as above.
For tiny specimens the use of a
high-quality macro lens or a microscope with digital camera is recommended.
Because such set-ups often do not allow a large depth of field, it may be
necessary to shoot focus stacks of photographs, i.e. take the same photograph
repeatedly but with a slightly different focus distance, and use dedicated
computer software to compute these stacks into individual images (note: the
final images should preferably have EXIF data, which you can add manually).
Turntable method for small mobile
specimens - without turntable
Use a sandbox or a very sturdy
piece of cardboard as a makeshift turntable (Figure 5). If this is not possible,
use a piece of white cardboard to blank the table surface (if you have any), set
the specimen on the table with a scale adjacent, take several photographs from
different positions, then begin the process of rotating the specimen to complete
the picture set as above. When processing, set in-program markers for scale on
the photos but mask the scale bar along with rest of the background (if masking
the latter is necessary).
Figure 5: Digitizing a small
specimen (caudal vertebra of Citipati in the AMNH collection) without a
turntable. A. Setup with camera on tripod, light source sub-parallel to camera
view and a cardboard box with sand as a makeshift turntable. Printed paper
serves as feature-rich background in case the specimen offers too few features.
A caliper serves as scale. In this case, the specimen offered ample points; see
Figures 10 and 11. No markers were put on the specimen due to its fragility;
easy model creation could only be realized using the one-chunk method. B and C.
Images from the two series, showing the two positions the specimen was placed
in. Note that a matchbook was used to prop up the specimen in B. All parts of
the surface were still adequately documented in several images, so that the
blocking of parts of the specimen from view in some images had no negative
consequences for model creation.
Turntable method: scale bars
The normal procedure for placing a scale bar is to put it next to the specimen,
on the turntable if one is used, and leave it there for the duration of the
photographing session. If it is necessary to move the specimen between
photographs that belong to one set, the scale bar should be removed at this
time, or it must later be masked along with the rest of the background in all
images taken after this time. A scale bar does not have to be modeled in 3D, but
must at least be present in two photographs. If it can be exactly marked in more
photographs, the overall accuracy can be improved. Several scale bars are better
than one, especially for very large specimens of which each photograph will show
only a part, as they reduce the measurement error. They should be placed on
opposite sides of the specimen, and can then help reduce distortion. The larger
the scale bar, the better, because the error caused by photograph resolution and/or
marker placement in the software becomes relatively smaller. Ideally, scale bars
get rotated with the object.
Even for the one-chunk method, any
scale needs not be in same relative position to the object after flipping over.
Theoretically, it is sufficient that a scale is present and fully visible in two
photographs of one set only, as long as it does not move relative to the
specimen between them, provided these two photographs align with the rest of the
set. However, more photographs should be taken to be on the safe side. Scales
should also always be included in the setup for the second (and any further) set
of photographs, in case the multi-chunk method must be used if the one- chunk
method fails (see below).
Turntable method: using
physical markers on specimens
If at least three markers are
placed on the specimen (see Figure 4) so that each is visible in two photos, the
markers can be used to align models calculated from each of the two (or more)
separate sets of photographs required to cover the whole surface (required for
the multi- chunk method). It is generally a good idea to place markers even if
the use of the one-chunk method is intended, as they greatly ease the task of
alignment of parts if the one-chunk method fails.
Because all markers placed on the
specimen will be visible in the final model, markers should be as small as
possible. Tiny pieces of white self- adhesive labels marked with the letter X
(use the crossing point of the two lines for the in- program marker) and a
number (for easier identification on the photos) work well, if care is taken
that the markers do not fall off when the specimen is flipped upside down. Make
sure to use only materials from which no chemicals can leach into the specimen,
and which do not leave any residue when removed.
Markers must be well visible in
all positions that the specimen will be placed in during photography. It is
advisable to turn the specimen over after placing them, to check if they really
are visible in the alternate positions.
It is possible to produce a marker-free
model with added effort, by taking additional photographs with the markers
removed, and masking the markers in all photographs. Care must be taken to take
a sufficient number of images, so that each spot that was covered by a marker is
well represented in sufficient detail in at least two additional photographs.
The marker- free images then provide the surface information for those parts of
the surface that is under the marker. However, because this approach involves
talking near-duplicate photographs, the calculation time for the model will rise
The walk-around method: basic
The walk-around method inverts the
roles of camera and specimen, in that the latter is stationary, and the former
moves. Thus, the obvious advantage of the walk-around method is that it allows
capturing completely immobile specimens, as well as those that cannot be placed
on a turntable or manually rotated. The disadvantages are lack of or limited
ability to control lighting, often a lack of line-of-sight onto parts of the
specimen (especially in exhibitions), the need to adjust camera settings for
each photograph, and an increased need to construct a mental image of the sum of
camera positions to judge if the specimen surface has been sufficiently captured.
Walk-around method: very large
or barely mobile specimens
If a specimen is too large, heavy or fragile to be placed on a turntable, but
can be otherwise moved (e.g. on a trolley), it is usually advisable to position
it so that there is room to move the tripod all around it (see Figure 6 for a
series of photographs taken with this method). Also, it is usually worthwhile to
spend some time searching for a position with good light.
Photographs should be taken so that the relative positions of camera and
specimen are roughly the same as in the protocol for using a turntable above.
The sole difference is that the role of the stationary part and the mobile part
are exchanged. As a consequence, the lighting, exposure time and depth of field
must be checked for each camera position separately. Care must be taken to avoid
reflections on the specimen caused by light sources such as windows behind it,
especially if it is covered by lacquer. There is no requirement for the camera
positions to be as regularly spaced as the use of a turntable will usually make
them. Figure 7 shows the sparse point cloud, camera positions and dense point
cloud generated from the photo set shown in Figure 6. Note how several different
elevations of the camera were used to ensure sufficient capture of the surface.
If additional lights are placed
they need to stay in place during the entire photography, as it is nearly
impossible to reconstruct their exact positions and directions during later
parts of the photography process. Alternatively, a set-up producing even light
can be moved with the camera, so that the entire view in each photograph is
evenly lit. Photography should be conducted rapidly to avoid changing light
conditions. It can be preferable to ignore people walking through, as they can
be masked. In such an event it is best to take more photographs.
Specimens too large to be moved at
all must be treated like in situ specimens outdoors, except for the restrictions
imposed by sunlight.
Walk-around method: in situ and
Specimens that are immobile can
only be photographed in situ by walking around them as far as local conditions
allow. This places restrictions on the lighting conditions, and may mean that
parts of a specimen cannot be digitized because the camera cannot be brought
into positions required to photograph them. Figure 8 shows an example of a
mounted dinosaur skeleton in an exhibit hall populated by obstacles in the form
of other exhibit specimens. Especially problematic are specimens outdoors, where
one is dependent on weather conditions, and often has no access to electrical
power available. Try to avoid strong sunlight as it causes high contrasts with
dark shadows (also true in exhibition spaces with natural light, such as the
AMNH dinosaur halls); use reflectors/flash to brighten them up. A light but
uniform cloud cover is preferable. Avoid shooting during times of day where the
sun shines at a shallow angle onto the surface of interest (i.e., for sub-
horizontal surfaces prefer shooting during mid-day, for strongly inclined
surfaces choose times accordingly).
When a specimen is subject to
changing light conditions, work rapidly to minimize the differences and ignore
people walking through view (they can be masked out; take more photographs to
ensure that all parts of the specimen are sufficiently captured).
Figure 6: Image set of specimen
Khaan mckennai IGM 100/1127 (currently stored at AMNH) on a trolley, set up in
the middle of the room so that there was space to move a tripod around the
Figure 7: Model of specimen Khaan
mckennai IGM 100/1127 (currently stored at AMNH) created from image set shown in
Figure 6. A. Sparse point cloud and camera positions. B. Dense point cloud in
same oblique view as A. C. Dense cloud, medium density. D. Closer view of the
skull. Note the regular arrangement of cameras in A caused by the identical
tripod height for several sets of photographs, and note the height lines in the
dense point cloud.
Mounted skeletons, long trackways
and similar very large and complex objects can be calculated in chunks and
merged later (see below). If this approach is chosen, the photography should be
adjusted by shooting series of pictures of parts, with markers for the later
alignment placed beforehand. Each part should contain its own scale bar, as
large as possible. It is for example possible to measure railings or other
architecturally defined distances. You may also use a complete measuring tape or,
otherwise, place a yardstick (ideally at least 2 m) next to each section of the
specimen in a stable position while you photograph it. To facilitate correct
photogrammetric calculation of repetitive pattern such as ripple marks on
trackways, place uniquely colored/shaped objects (e.g., clothes, tools, etc.)
around the specimen. Typically, specimens with complex shapes in exhibition
settings suffer from uneven lighting caused by top-down light or spotlights,
causing strong shadows on the undersides of individual elements. Ground-mounted
spotlights sometimes ameliorate this effect, but are normally insufficient to
allow straightforward digitizing. If possible, ask for access outside normal
visiting hours, and for the exhibition lights to be turned off. Many museums
have “cleaning light” that more evenly lights the specimen. Use reflectors and
additional light sources, and use a flash if nothing else helps. A second,
hand-held and automatically triggered flash can also be helpful. If nothing else
works, block spotlights or reflections with your hand (Figure 3C).
The actual process of photography
consists of moving around the specimen and taking photographs. As simple as this
sounds, there are a number of pitfalls. First of all, it is important to retain
enough overlap between images, especially if the view of the specimen is edge-on.
Here, it is even more important than in the turntable method to shoot more
images than one believes to be necessary. Care must be taken to not shoot
panorama series (in which the camera is pointed in different directions but
remains stationary), as these image sets have little to no parallax between
individual images. For huge specimens, especially those too large to fit
entirely in each photograph, e.g. because it is impossible to gain enough
distance or because a higher resolution of the model is required, it can help to
place visual markers of used positions on the ground, e.g. small pieces of paper,
so that one can keep an overview of what has already been photographed.
Figure 8: Four views (A. anterior,
B. lateral, C. top, D. oblique) of sparse point cloud and camera positions of an
image set of the torso of the Museum für Naturkunde Berlin Diplodocus mount in
the Dinosaur Hall. Note how the neighboring Giraffatitan and Dicraeosaurus
skeletons have also been captured, and how they block line-of-sight to the right
side of the Diplodocus mount (gaps in camera positions at the top of C). Also,
the other specimens and the pedestal they rest on require variations in the
distance between camera and specimen. Note how the tails and necks of the mounts
are badly represented in the sparse point cloud, because they are captured only
on the fringes of some images. In this example, erroneous feature matching leads
to sub-optimal alignment, causing increasingly visible distortion with
increasing distance from what roughly is the focal point of the image set (the
torso of Diplodocus), especially notable on the right lateral sides of
Dicraeosaurus and Giraffatitan in the top view
Exposure must be checked and
adapted for each photograph, as differences can easily cause color differences
which make feature matching difficult for the program, degrading or failing
alignment. It may even be necessary to adjust the white balance between shots.
RAW format photographs, in which settings can be developed later, can be useful
under these circumstances. Especially outdoors, but also in indoor places with
low-mounted light sources, it is important to avoid casting shadows on the
Also, it is often difficult to
capture the top surfaces of huge specimens sufficiently from ground level. In
this case, arrange for a ladder and a second person to steady it. Long
telescopic masts, the use of kites or UAVs (Unmanned Aerial Vehicles; e.g. Watts
et al. 2012; see http://www.mikrokopter.de) are useful while photographing large
Walk-around method: specimens behind glass
Museum specimens on exhibit behind glass present an especially difficult case
for photogrammetry, because typically the glass is not perfectly clean and
reflects lights and well- lit structures (Figure 2A). These reflections
interfere with model creation. Often, a polarizing filter can remove most of the
reflections (Figure 2B). Placing the camera very close to (ideally almost
touching) the glass and careful observation of the focus point usually makes the
dust and grime layer on the glass invisible on the photos (Figure 2B). At worst,
a separate flash held at an acute angle (combined with a camera placement very
close to the glass) can be used to reduce the relative strength of reflections,
by lighting the specimen so much that the reflections are outshined. One also
may use optically dense materials like a hand or a piece of dark cardboard to
block reflections (Figure 3C).
Walk-around method: scale bars
The normal procedure for placing a scale bar is to put it next to the specimen
and leave it there as long as the photographing session takes place. If it is
necessary to move the specimen between photographs that belong to one set, the
scale bar should be removed at this time, or it must later be masked along with
the rest of the background in all images taken after this time.
Walk-around method: using mirrors
If it is physically impossible or impracticable to place the camera behind the
specimen, e.g. when a specimen is mounted close to a wall, it is sometimes
possible to place a mirror behind it. Photographs can then be taken of the
specimen in the mirror, and later treated like any other photograph in the model
creation phase. The same approach can be used for photographs from below. Make
sure to take a sufficient number of photographs with sufficient overlap to those
taken without the use of a mirror so that alignment is possible. Because it is
not always possible to fill the frame with only the mirror additional masking of
photographs may become necessary.
It is not necessary to mirror
photographs taken using a mirror in a photograph editing program before they can
be used in photogrammetry. A mirror simply re-directs light, so that the
calculated camera position is the hypothetical location from where the camera
would see the object as it is shown in the photograph.
Background – blank or structured?
The background behind and especially under the specimen has a profound influence
on the model building phase. If the program detects features on it, these points
can be used in the alignment of the photographs, where they often play a helpful
role because of the large parallax-induced motions they experience between
photographs. The features will result in points being created in the dense point
cloud, and accordingly polygons in the polygon mesh. As such points and polygons
are typically not desired and must be cropped, a feature-rich background and
support for the specimen typically means an increase in work time. Alternatively,
the background must be masked by hand in all photographs, taking often even more
time. For specimens on a turntable features on the background make masking
mandatory as they otherwise impede the alignment process.
A blank and out-of-focus
background means no masking or cropping is necessary and makes the one-chunk
method easier to use, but may decrease the chances of a successful alignment
within a set of images. Therefore, the effort in time and money necessary to
mask photographs must be weighed against the effort of re-shooting a specimen
for which modeling fails. If a specimen is accessible only during a special
occasion, or if the cost of re- shooting is high due to travel costs, we
recommend using a structured background that can help with alignment. On the
other hand, easily accessible specimens should be photographed using a blank and
out-of-focus background. The example shown in Figure 5 shows the use of a
structured background, because the cost of another intercontinental trip far
outweighs the effort of masking about 2000 photographs taken during the visit.
In fact, the vertebra shown in Figure 5 aligned well using the one-chunk method,
but other, smaller vertebrae from the same series required the use of background
features for alignment.
A background that allows easy distinction of features by a human, such as a page
of printed text (easily available anywhere), also allows the manual placement of
markers to aid the alignment process, and is therefore better than a
feature-rich but difficult to assess wild pattern.
Photography tips & tricks
Do not use a camcorder
Although photogrammetric models
can be calculated from video frames, it is not recommended because motion blur
does not permit crisp images and reduces the quality of the resulting model.
Easier photography with a tilt
A DSLR with a rotatable (touch-)
screen and live view that shows the view of the lens before the shutter is
pressed (e.g. Canon EOS 650D; Nikon D5100) makes it simpler to choose the best
focal point, and allows speedier and easier photography in cases where the
camera has to be held very high or low, or over a barrier.
Keeping photograph series apart Sorting the thousands of photos from a single session is most easily
achieved by using the large thumbnail folder view. In order to identify each
series of photographs speedily, it is advisable to write down the first and last
image numbers, or to photograph before and after the series a piece of paper
with the specimen number and potentially other useful information (i.e., “back
set”, “part 1”, etc.) as shown in Figure 4. This paper can be held in front of
the camera when it is mounted on the tripod, so no time is lost altering the
camera position. The text should be written with a dark marker thick enough to
be readable in the file explorer thumbnail view.
When series are separated into
sub-folders, these photographs should be moved with them.
Review and remove bad and redundant images because too many photos may overwhelm
the software. Select only high-confidence information for processing. If the
background interferes with alignment, mask it out. Also, even when using the
multiple-chunk method, it is often faster and easier to mask the background than
to remove erroneous points from the finished model.
If the alignment is not correct
for a certain image, re-set and re-run or delete it. Human brains are still
smarter at filtering than the software. Check the camera position display (e.g.,
Figures 7, 8 - all camera positions are fine, and Image 9 - three positions are
obviously faulty) for images that were supposedly taken 'inside' the specimen,
from below the floor, or from unrealistic distances. Photograph sets taken with
the turntable method should align in perfectly regular circles, and images taken
at identical tripod heights must be on one level.
Also, if the set contains many
photographs, consider using only a subset for the model. Using more images not
only increases the total calculation time, but can also lead to artifacts on the
surface. If images are redundant, tiny and unavoidable inaccuracies in alignment
will lead to the program finding several points with minimal differences in
position where there only should be one point. As a consequence, the surface can
become wrinkled, may contain pyramid artifacts caused by individual points
floating just above or below the rest of the surface, or may even be created as
two sub- parallel instances.
If a project is very large it can
be a viable alternative to split it into chunks (see below). Each chunk should
contain images that overlap well. For example, if a mounted skeleton of an
elephant is to be modeled, one chunk could hold the skull, neck and front limb
images, another the hind limbs, and a third the main body. Once the images
within each chunk are aligned, the chunks can then be aligned via markers (see
Scaling the model
Scaling needs to be done manually, because the methods suitable for
paleontological digitizing usually do not allow the use of targets with scales
that the software can recognize automatically. Therefore, at least one object of
exactly known length must be visible in at least two of the photographs of one
set, and may not move relative to the specimen between the two images. It is
important that the two ends of the known distance can be found with ease on the
photographs. Therefore, measuring a distance on the specimen is not recommended,
unless it is between two tiny discrete marks. For example, the 'maximum length'
of a bone cannot be used because it will be nearly impossible to identify the
two measuring points down to one pixel in the photographs. We recommend using
printed scale bars or (folding) yard sticks marked in centimeters (practically
all photogrammetric software uses the metric system). It is usually best to
place in-program markers on the images, not the 3D model or dense point cloud.
1. Create one marker at one end of the scale object and place the same on a
2. Create a second marker at the other end of the scale object and place the
same on another image. Note that it is not required that both the first and
second marker are created on the same image, nor is it necessary to use the same
second image for placing the second instance!
3. Use the two markers to create a scale bar.
4. Set the length for the scale bar.
5. Repeat for as many scale objects as are available.
Note that in Agisoft Photoscan Pro the scaling step can be prepared before the
Alignment, but can also be performed after the images have been aligned, via the
Undesirable parts of photographs containing moving objects or repetitive
background features cannot always be avoided. Such areas need to be made
unavailable for feature detection; otherwise they can ruin the alignment and
model creation processes. Masking can be performed in several ways: in a
graphics program, where the area can be blanked (any uniform color will do)
manually by painting in or lassoing, or automatically using a magic wand tool.
We have found, however, that a very uniform background suitable for use of a
magic wand tool usually is so constant that it does not allow the photogrammetry
software to pick up features anyway, and thus needs not to be masked. The second
option for masking is the in-program masking of the photogrammetry program.
Figure 9: Top view of sparse point
cloud and camera positions calculated from an image set of Dimetrodon mount at
the Royal Belgian Institute of Sciences, Brussels. Camera positions that are
nonsensical (inside the mount’s skull) or a massive mismatch to the images (almost
in touch with fore- and hind limbs) are highlighted in red.
In both cases, the exact
separation of desired and undesired data is important. There is a natural
tendency to draw the mask so that all parts of the specimen are retained in the
un- masked area. The direct consequence is that the contact area between the
specimen and the background is in smaller or larger parts also contained in the
allowed area, and will be used by the photogrammetry software. However, there is
no 100% clear distinction of the 'this pixel is specimen, the next one is
background' kind. Therefore, drawing the masking line this way will have pixels
included in the alignment and model creation that contain information that is
not strictly speaking part of the specimen. Usually, if the rim of included
background and contact area pixels is narrow, the effect will be minimal, and
amounts only to a small number of erroneous points floating close to the main
model. In the end, it comes to a tradeoff between time spent masking and time
spent removing artifacts from the dense point cloud. However, it is easy to
avoid the creation of these points by simply masking the border area with the
background, i.e. by leaving only those parts of the image un- masked that show
only the specimen (Figure 10). Similarly, dark shadows on the underside of
specimens can also be masked, resulting in more realistic textures, provided
there is sufficient overlap within the remaining photograph parts.
If features on the background are
needed to achieve good alignment of the images, it is still recommended to mask
a thin strip of pixels around the specimen, especially in places where the
specimen contacts the ground. This strip will later result in a gap in the dense
point cloud that makes cropping the undesired background points easy and fast.
Although running the alignment can
be as easy as simply choosing the corresponding step in the program menu, there
are settings that can have a strong influence on the quality of the resulting
Figure 10: Image of a caudal
vertebra of the oviraptorine dinosaur Citipati osmolskae IGM 100/978 (currently
stored at the AMNH). A. Masked image. Note that the markers used for scaling the
model can be in the masked area. B. Points marking detected features in the
image. Note how no features are detected in the masked areas
Figure 11: Model creation process
with the one-chunk method on the example of a caudal vertebra of the
oviraptorine dinosaur Citipati osmolskae IGM 100/978 (currently stored at the
AMNH). A. Aligned images and sparse point cloud. Each blue rectangle shows one
reconstructed camera position with the matching image filename. Note that the
two circles of photographs are not sub-parallel to each other, as the geometry
of the specimen did not allow rotating it by ~180°. However, all parts of the
surface are sufficiently captured to deliver a complete model. Two markers were
used to set scale (see Figure 10). B. Closer view of the sparse point cloud with
127,994 points. Because of extensive masking in all images there are no points
representing the background. C-D. Dense point cloud with 5,733,491 points with
(C) and without (D) color. E-G. Polygon mesh with 7,108,439 vertices and
14,216,842 polygon faces with color (E), shaded (F) and wireframe display (G).
H-K. Polygon mesh reduces to (H) 1,500,018 vertices and 3,000,000 polygon faces,
500,012 vertices and 1,000,000 polygons (I), 50,006 vertices and 100,000
polygons (J) and 5,000 vertices and 10,000 polygons (K). L. Photograph of the
The regular approach should always be the use of the highest quality alignment
the program offers. However, if this approach fails, it is recommended to use a
low-quality setting initially, eliminate the images that are obviously mis-aligned,
and re-run the alignment at high quality. Similarly, the number of points the
program is supposed to use for the alignment can be increased at the cost of
much longer calculations times. Increasing the number per image three- to
five-fold can, however, rescue data sets that otherwise do not align at all.
Lastly, choosing generic pair-selection (if available in your software) can also
help to achieve better alignment.
Additionally, it is always worth
checking the points display for all images (Figures 3B and 10B) to see if
erroneous points are being used in the alignment. Such points can be on parts of
the image that should not be used, e.g. background that was insufficiently
masked, or can be on parts of the image that should be used but produce
false-positives in the search for identical features. Typical for the latter
case are points on building parts or other repetitive structures in the
background, or points on repetitive features on the specimen itself. The former
can be avoided by masking, the latter can be ameliorated by the method described
in the next paragraph.
The last resort, when a photograph
set that finally fails alignment cannot be easily re- taken, consists of adding
in-program markers manually to some or all images that align well with each
other and to all images that do not align well, and re-run alignment. Depending
on the reasons for the non-alignment this method can sometimes lead to perfect
alignments for a tolerable amount of work, or can require several dozens of
markers to be placed on hundreds of images, a task that is usually impractical.
In this case it may be a viable alternative to split the project into chunks,
and use markers to align the chunks.
Alignment methods for more than
one set of images
Method 1: one-chunk (preferred).
Summary of photography method suitable for one- chunk method: One set of
photographs on turntable, flip specimen over, take second set. Repeat until the
entire surface is well represented in the photograph sets. Include scale bar in
each set. Try to make background unsuitable for detection of points: use
featureless materials, distance specimen from turntable (place on perspex cube;
cover turntable with white cardboard; covering with white or black cloth
possible but may have enough structure to give points). Set depth of field so
that full specimen but not background/turntable is in focus. Blank or out-
of-focus background can make masking unnecessary.
See Figure 11.
1. Add all sets of photos to one
chunk, including the photograph that separates the two sets. Make the latter
unavailable for alignment; it only serves as an easy clue in the photo list to
distinguish the two sets.
2. Add markers to the scale bar in
one or both sets, create in-program markers and the scale bars and set the
3. Mask the entire background in
all photographs, including the scale bars (those parts of the background on
which no points can be detected can be omitted from the masking). The more
accurately the masking outline follows the specimen outline, the better the
final model will be and the fewer erroneous points will be created along the
edges of the model (this step may be unnecessary if no points are found on the
background. Run a test alignment with a low number of photos and a high point
detection number to check).
4. Align the photos, optimize for
all scale bars as described above.
5. Generate a dense point cloud.
This point cloud should then be inspected for erroneous points along the areas
where the model is based on one set of photos; typically, this area features
some dark points that pertain to areas outside the specimen, and stem from
erroneous points found in the shadows the specimen cast on the table. If the
masks in the photos reach very close to the specimen, there will be few such
points. Small numbers of erroneous points can however be ignored as their
influence in polygon mesh creation is negligible.
6. Generate the polygon mesh.
If the one-chunk method fails, use
the multi- chunk method on the same photographs. Only if this method also fails
will it be necessary to take more photographs.
Method 2: multiple-chunk. Summary
of photography method suitable for multiple- chunk method: one set of photos (with
or without turntable), flip specimen over, take next set (repeat if necessary).
Include scale bar in each set. For walk-around method of large specimens: Take
one set of one end of the specimen, take a separator photograph, take set of
next section, ensuring that the two sections overlap. Repeat if necessary. See
The multi-chunk method allows
using the background for the alignment step within each chunk (those parts of
the background that do not move relative to the specimen during the photography
of one set of photos), thus it is a good method for specimens where few points
for alignment will be found on the specimen itself. A background well suitable
for point detection should be chosen (newspaper, Persian rug, etc.). Also, using
the multi-chunk method means less care is needed to set up the turntable than
for the one-chunk method, and the preparation in the photogrammetry program is
easier, as background blanking or masking is not needed. However, much fiddling
may later be necessary to adjust the alignment between the two chunks, or the
fit between the two model halves. The method also makes handling very large
projects easier, by reducing the overall calculation time and improving the
chance at good alignment. The method works with more than two series of photos
and shells as well, but more parts usually mean more trouble aligning them.
Figure 12: Model creation process
with the multi-chunk method on the example of a fibula of a sauropod dinosaur
from the Utah Field House of Natural History State Park Museum in Vernal. A.
View of the program interface of Agisoft Photoscan Pro with (left) the chunks 1
and 2 containing the two image sets. Note that markers have been added to both
sets. Markers called ‘X 1’, ‘X2’ and ‘X 4’ in both chunks mark the positions of
the physical markers on the specimen, as seen on the display of the image (right).
Additional markers (‘point 1’ through ‘point 4’) in chunk 2 are intended for the
creation of scale bars. B. From the additional markers (circled in red) four
scale bars have been created (circled in orange), and their lengths set. Via the
“wizard wand” button on the top left an existing alignment can be refined to
include the scaling information. Alternatively, the scale bars can be added
before alignment. In this case, the sparse point cloud for chunk 2 is shown on
the right. C. The two chunks have been aligned based on the markers with
identical names, and merged. The new chunk ‘merged chunks’ contains all images
and all markers (green circle). Note that the merged sparse point cloud shows
slight alignment problems on the lower left edge of the bone shaft near the two
markers ‘X 4’. However, the near-perfect alignment of the markers, so close that
in the model view they differ by less than three pixels each, shows that each
individual set of images was well- aligned (otherwise the 3D placement of the
makers would not fit the other set). D. Dense point cloud computed from the
merged sparse point clouds. Note that there are a number of artefacts around the
edges of the bone, but that the overall shape of the bone and most details are
well represented. Compare C to Figure 13.
Figure 13: Sparse point cloud from
the same image sets as in Figure 12, but computed with the one-chunk method.
Comparison to Figure 12 C shows that the one-chunk method here results in a
large number of alignment problems. The most obvious resulting erroneous points
are circled in red.
As in the one-chunk method, it is
possible to mask the background for a cleaner model provided the features
detected on the specimen itself suffice for alignment within each image set. In
the example shown in Figure 12 this is the case; but barely: several images are
not entirely correctly aligned (visible by the handful of ‘floating’ points in
the lower left quadrant next to the bone shaft; caused by slight misalignment of
several images). If the same data set is run via the one-chunk method, the
alignment is less good (Figure 13).
In order to ameliorate the
fiddling necessary to align the chunks, it is advisable to mark the specimen
with points that can be used to place markers with high accuracy (Figure 12A).
Three markers are the minimum necessary, more are advisable. However, the
markers will be visible in the texture of the finished model. If two separate
dense point clouds are generated and later combined in a different CAD program,
there typically will be artifacts from a sub-perfect fit of the two halves and a
lot of manual correction is needed.
1. Add each photograph series to a
separate chunk in one overall file.
2. Add markers to the scale bar in
one or both sets, create the scale bars in the program and set the appropriate
length. Note that the markers used to create the scale bars should have
different names in each chunk, as they will otherwise be included for a marker-
3. Mask in all chunks only those
parts of the background that move relative to the specimen, or mask the full
background if you expect the specimen to deliver sufficient features for
4. Align the images in all sets
(use batch process).
5. Place markers on the
photographs on the physical markers you put on the specimen. Rename the markers
so that the markers corresponding to the same physical marker have the same name
in all chunks. Leave one physical marker unused; it can later be used to check
the chunk alignment.
6. Align the chunks, marker-based.
Alternatively, align them
point-based, if all background in all photos has been masked.
7. Merge the chunks.
8. Add a marker to the previously
unused physical marker in two photographs, and check its position in all other
photographs. If there are systematic divergences, one chunk is not well aligned.
Note that such misalignment may be obscured on the model!
9. Remove background points in the
sparse point cloud of the merged chunks.
10. Calculate the dense point
11. Remove any remaining
background points from the dense point cloud.
12. Calculate the polygon mesh.
Very large specimens (trackways,
excavations, mounted skeletons).
The calculation time for alignment,
dense cloud generation and mesh creation increases exponentially with the number
of photographs used. If the vast majority of photographs overlap with a
significant portion of other photographs nothing can be done to accelerate the
process. If, on the other hand, each photograph overlaps only with a handful of
others, as is the case if a long sequence of photographs documents a large area
such as a trackway, the set can be split into chunks that each calculate quickly.
If the alignment is performed in chunks, these can later be merged based on
markers, as described above for the multi-chunk method, which takes little time.
To ease this task it is useful to place numbered markers before the photography.
Tracks, for example, may be photographed with scale bars next to them and a
piece of paper carrying a number. Later, distinct points on the scale bars can
easily be used to create in-program markers for chunk alignment. Additionally,
for large numbers of photographs it is usually worthwhile to turn on generic
pair selection which filters out those photos that likely overlap for alignment
and discounts all other photo pairs, thus reducing the calculation time
For dense point cloud and polygon
mesh generation it is similarly advisable to select only a section of the entire
model, calculate the dense cloud and mesh, save to a new file name (e.g., the
name of the entire file with ‘_part01’ appended), select the next part,
calculate the dense cloud and mesh and save with a new name (‘_part02’), and so
on (Figure 14). Alternatively, in the program the box used for selecting the
volume for dense cloud computation can be moved ahead by dragging a corner point
from the beginning of the model past the points marking the end of the first,
already calculated dense cloud part, so that the borders between dense clouds
are an exact touch without any gap or overlap. This process results in
manageable file sizes, but each partial dense cloud is aligned with all others,
and most research tasks can be performed by alternately using the individual
In order to scale large models at
high accuracy it is best to include markers at the far extremes of the specimen
and measure their physical distance in the field with a measuring tape. For
aligning several versions of models based on photograph series from different
times, e.g. to document the advance of an excavation and the relative position
of bones removed at different times of the digging season, or even across
several seasons, it is advisable to place several immobile and clearly visible
markers (e.g. chisels or poles cemented in drilled holes).
If large complex specimens were
photographed in chunks, the multi-chunk method described above can also be used
for alignment. For segmented specimens (e.g. skeletons) it is advisable to
calculate the dense point clouds for the separate chunks after alignment, as
editing is much faster when done on smaller overall point clouds. Instead of
merging all chunks (step 7 above), the chunks can be kept separate and only the
finished polygon mesh models of the individual segments should be combined into
one file, usually in the separate CAD software used for further processing.
Using remote computing
If remote computing is available, it can speed up the calculation of
photogrammetric models considerably. However, not all processes during the
creation of a 3D-model are equally suitable for remote computing. It is
recommended to finish all CPU-heavy steps (alignment, dense point cloud
generation, polygon mesh generation) on remote, while all interaction heavy
steps involving a lot of data loading (masking, marker placement, point cloud
and mesh editing), and thus on a remote computer a lot of data transfer, should
be carried out on a local computer.
Additionally, for all programs
offering batch processing, it is advisable to set up batch operations that run
autonomously, e.g. overnight. Although sometimes steps have to be repeated
later, e.g. because the program does not automatically set crop parameters
appropriately for dense point cloud calculations, the avoidance of idle time is
usually a significant gain in overall work speed. If available, a save-after-each-step
option should be used. It allows interrupting calculation of large batches with
minimal loss of completed work.
Figure 14: Trackway of a theropod
dinosaur in the Wesling Quarry in Münchehagen, Germany. A. Oblique view of
sparse point cloud and camera positions calculated from 86 images. B. Roughly
top view of sparse point cloud. C. and D. show piecemeal creation of meshes of
only the key areas. In C the area around a single footprint has been selected
for mesh generation (denoted by red points), in D the selection area has been
shifted to the next footprint. E. Rhinoceros 5.0 (McNeel Associates;
www.rhino3d.com) view of all separate meshes. Note how the separate meshes are
all to the same scale and in correct relative position to each other, although a
complete dense point cloud or mesh of the entire trackway was never calculated.
The total file size (as Stanford PLY) of all tracks is under 100 MB, whereas a
mesh covering all of them together would be over 1 GB in size before cropping.
We estimate the time saved at about 70% compared to calculating one single huge
mesh and cropping it.
Tips & Tricks
Specimens that are flat are best
not placed on the two flat surfaces, because each set of pictures then captures
the flat surface perfectly, but the area with high curvature connecting the flat
surfaces is usually captured (and thus reconstructed) less well, with little
overlap between the two photograph sets. It is therefore advisable to place the
specimens on edge on a support (e.g. on modeling clay; remember to use a plastic
film so that no chemicals from the clay contaminate the specimens), so that the
flat surfaces are vertical. When the flat surfaces face the camera, large angles
can be covered between photographs; whereas the edge-on positions require small
intervals (<5°). This setup creates large overlap between the two picture sets
showing the flat areas, ensuring excellent alignment and model creation.
Specific, irregular shaped objects, such as dinosaur ulnae, tend not to rest in
two positions that are roughly 180° from each other. In such cases, it is
advisable to take three or more sets of photographs, using the minimum number of
positions the bone can easily be placed in. Both the one-chunk and the
multiple-chunk method can be used, but it is always worth the extra trouble to
take photographs suitable for the one-chunk method, as the time invested in
aligning many chunks in the many-shell method is usually significantly higher.