$499 (USD)

per year, per user

Academic Price :
$249 (USD)


The Most Used 3D Shape Analysis & Morphometrics Software in the World

Used by thousands of researchers at hundreds of top research institutions and museums around the globe, Checkpoint is an integrated software package for geometric morphometrics that enables you to easily collect, manipulate and analyze thousands of landmark and semi-landmark points in 3D. In seconds, it loads both surface meshes and volumetric scans for use in shape analysis, shape modeling and diagnostic imaging.

Checkpoint’s user-friendly 3D landmark editing interface empowers you to quickly place single points, curves and patches to represent even the most complex specimen morphology. This state-of-the-art tool gives you the ability to inspect, perform statistical analysis and virtually manipulate, and measure every anatomic feature on laser-scanned surfaces or within micro-CT, CBCT, CT or MRI scans.

Checkpoint is the world leader in 3D shape analysis and morphometrics because nothing else:

  • Offers as many capabilities
  • Is as easy to use
  • Works as fast
  • Measures every anatomic feature within your scans
  • Works seamlessly with laser-scanned surfaces, micro-CT, CBCT, CT and MRI scans
  • Saves you as much time

Find out for yourself why Checkpoint is the world’s leader in 3D shape analysis and morphometrics.

Citing Checkpoint in Academic Publications? Click Citations below.

Checkpoint Demo

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Collect Landmark Points:

  • Place landmark points, curves, and patches.
  • Automatic generation of semi-landmark points along curves and patches.
  • Export landmarks to common file formats.

Load Volume and Surface Data:

  • Load DICOM scans (DCM files).
  • Load PLY, STL, OBJ, and WRL surfaces.
  • Extract multiple isosurfaces from volume (DICOM) scans (and export them).

View and Interact in 3D:

  • 3D multi-planar reconstruction.
  • Axial, coronal, and sagittal slicing.
  • 3D volume rendering.
  • View slice-surface intersections.


  • Convert volume data (DICOM .DCM, NifTI .NII, Analyze .HDR, .VTK) to NII format.
  • Convert surfaces from one format (STL, PLY, OBJ) to another.
  • and more...

Download Stratovan Checkpoint 32bit or Stratovan Checkpoint 64bit today!

Additional Info



DICOM (.dcm)
TIFF Image Stacks/Series (.tif)
JPEG Image Stacks/Series (.jpg; .jpeg)
NifTI (.nii) 
ANALYZE (.hdr)
FITS (.fits)
Kitware VTK (.vtk)
(more to come)

PLY (.ply)
STL (.stl)
OBJ (.obj)
WRL (.wrl)

Export or Convert

IDAV Landmark (.pts)
PLY (.ply)
STL (.stl)
OBJ (.obj)
NifTI (.nii)
FITS (.fits)

Note: if you need a particular file format, please let us know and we'll do our best to add it.

Single pointPlace a single point landmark point at biologically relevant locations.
CurvePlace two or more points and automatically generate several semi-landmark points along the curve.
PatchPlace a grid of points to cover large regions. The edge points and middle point can be moved to give flexibility to the patch shape.
JointPlace two opposing homologous patches of points on two opposing joint surfaces to collect a matching set of points that can be used to analyze joint congruence.
LengthPick two points and compute the length between them.
AnglePick three or four points (two lines) and compute the angle between them.
PlanePick three or four points to compute a reference plane through them.
3D ReconstructionPerform a multi-planar reconstruction of 3D medical data from CT and MRI scans.
Volume renderingVarious interactive volume visualization are provided to explore your volumetric data.
Surface extractionExtract multiple iso surface from your volumetric data, export the surfaces, and/or place landmark primitives (points, curves, patches, etc.) on them.
Surface renderingInteractive surface rendering or loaded surfaces or extracted surface from DICOM data.
InteractiveIntuitive, easy to use interfaces, that allow you to interact with your data.

Checkpoint for Anthropology 

Extract Surfaces from CT Scans
Load DICOM, NifTI, TIFF Image Stacks and more. Extract 3D surfaces and export them as STL, PLY, and OBJ files.
Large SurfacesWorks with large surfaces containing millions of triangles (> 2M).
Geometric MorphometricsEasily collect thousands of landmark points on dozens of specimens. Checkpoint's easy to use landmark editing tools allows you to gather numerous 3D points faster and more accurately than other tools.
Generalized Procrustes AnalysisPerform sophisticated 3D statistical analysis based collected points including statistical shape, morphometric, and procrustes analysis.
Statistical Shape AnalysisExport collected points from Checkpoint for use in other popular analysis tools.
3D Visualization and Measurements
Easily view, interact, and understand your specimen. State of the art visualization tools allow you to inspect, manipulate, and measure every anatomic feature.
IDAV Landmark Editor
Checkpoint is designed and built by the same team that developed the popular IDAV Landmark Editor software. Checkpoint allows you to work with CT (and MRI) scans and provides more flexible landmark collection tools.

Checkpoint for Medical 

CT, MRI, PET, and more.View 3D scans from a variety of modalities. Checkpoint creates a full 3D reconstruction and easily slices through the 3D reconstruction allowing you to see orthogonal and oblique slice views. Change brightness and contrast and easily interact in 3D.
3D Visualization and Measurements
Easily view, interact, and understand your patient. State of the art visualization tools allow you to inspect, manipulate, and measure every anatomic feature. Includes both 3D volume visualization and surface rendering.
Shape Analysis and Longitudinal StudiesEasily specify anatomic landmark points to measure complex features, such as a tumor size. Measure over time to determine and accurate growth (or shrinkage) curve. Checkpoint's easy to use landmark collection tools allows you to gather numerous 3D points faster and more accurately than other tools.
Statistical AnalysisPerform sophisticated 3D statistical analysis based collected points including statistical shape, morphometric, and procrustes analysis.
Extract Surfaces from CT Scans
Load DICOM, NifTI, TIFF Image Stacks and more. Export surfaces as STL, PLY, and OBJ files.

It works beautifully! I could not find any other program to open CT files and landmark in 3D. It has been an absolute lifesaver. I also appreciate that new versions are always coming out, with bugs fixed and great new features. Lastly, the customer service has been outstanding. I always receive a helpful and timely response, which has even extended to a quick program update in response to a bug I was struggling with. Excellent! Thank you!!! Checkpoint has made my dissertation possible.

Jessie, PhD Student at UC Berkeley

I use Checkpoint for viewing and adding landmarks to 3D models from CT of primate skulls, 3D models from MRI of the primate brain, and also 3D laser scanned models I have taken with a surface scanner. I like its versatility but with no comprise to ease of use. I like its flexibility, great graphics, speed and ability to handle larger data files.

Alannah Pearson, Phd Student at Australian National University

I really like this software and have recommended it to others. The patch placement method is very good compared to other pieces of software and curve placement is also very user-friendly. Customer support has also been excellent.

Katharine Balolia, Research Associate In Human Evolutionary Biology at George Washington University
Preview Images

Specimen loading interface. Load PLY, STL, OBJ, and WRL surface files in addition to DICOM scans (CT and MR). Browse to a folder and Checkpoint searches for data files (including subfolders). Search the specimen list easily by typing in a search.


Volume rendering of a DICOM scan. You can either view the volume rendering of a DICOM scan, change contrast and brightness by left-dragging the mouse in the slice windows. The data distribution histogram is show along the right side of the 3D window.


Surface rendering. Multiple surfaces can be extracted from DICOM scans by CTRL-left-clicking on the data histogram. Landmark points can then be added to each surface. Change between them easily by selecting them.


Edit landmark primitives. Change the semi-landmark point distribution density for curves and patches, view length and angle measurement, change primitive order, add names, or delete primitives.


Preview Videos

How to extract iso-surfaces from volume data.

How to work with single point primitives.

How to work with curve primitives.

How to work with patch primitives.

Related Publications

Rühr, P.T., van de Kamp, T., Faragó, T., Hammel, J., Wilde, F., Edel, C., Frenzel, M., Borisova, E., Baumbach, T., Blanke, A. (2021): Juvenile ecology drives adult morphology in two insect orders. Proceedings of the Royal Society B 288: 20210616.

Related repositories are here:
This ImageJ/Fiji macro converts an image stack directly into the *.ckpt and *.tif files needed by Checkpoint. The downscaling is now in its own script where other non-Checkpoint-specific tasks like rotation and cropping are done as well (
This reads in the landmarks from a *.ckpt file to skip the export function within Checkpoint which sometimes takes a bit to load with hundreds or thousands of large scans. Single Points and Curves are dealt with correctly, however Patches, Joints, and other primitives have not been tested.

Kraatz B, Sherratt E. (2016) Evolutionary morphology of the rabbit skull. PeerJ 4:e2453
Pearson, Alannah, Groves, Colin, Cardini, Andrea, (2015). The ‘temporal effect’ in hominids: Reinvestigating the nature of support for a chimp-human clade in bone morphology, Journal of Human Evolution
Ikeda, Renie, (2014). Clinical Application of a Novel Three-Dimensional Analysis to Evaluate Temporomandibular Joint Space Changes After Orthognathic Surgery, University of California, San Francisco.
Kuzminsky, Susan, Gardiner, Megan, (2012). Three-dimensional laser scanning: potential uses for museum conservation and scientific research, Journal of Archeological Science, 39, 2744-2751.
Bastir, Markus, Rosas, Antonio, Gunz, Philipp, Peña-Melian, Angel, Manzi, Giorgio, Harvati, Katerina, Kruszynski, Robert, Stringer, Chris, Hublin, Jean-Jacques, (2001). Evolution of the base of the brain in highly encephalized human species, Nature Communications, doi:10.1038/ncomms1593.
Lysianna Ledoux, Myrium Boudadi-Maligne, (2015). The contribution of geometric morphometric analysis to prehistoric ichnology: the example of large canid tracks and their implication for the debate concerning wolf domestication, Journal of Archaeological Science, 61, 25-35.
Aida Gómez-Robles, José María Bermúdez de Castro, María Martinón-Torres, Leyre Prado- Simón, Juan Luis Arsuaga, (2015). A geometric morphometric analysis of hominin lower molars: Evolutionary implications and overview of postcanine dental variation, Journal of Human Evolution, 82, 34-50.
Marta San Millán, Antigoni Kaliontzopoulou, Carme Rissech, Daniel Turbón, (2015). A geometric morphometric analysis of acetabular shape of the primate hip joint in relation to locomotor behavior, Journal of Human Evolution, 83, 15-27.
Ahmet Uzun, Fikri Ozdemir, (2014). Morphometric analysis of nasal shapes and angles in young adults, Brazilian Journal of Otorhinolaryngology, 80, 397-402.
Makedonska, Jana, Wright, Barth W., Strait, David S., (2012). The Effect of Dietary Adaption on Cranial Morphological Integration in Capuchins (Order Primates, Genus Cebus), PLoS One, doi” 10.1371/journal.pone.0101378.
Tschopp, Emanuel, Russo, João, Dzemski, Gordon, (2014). Retrodeformation as a test for the validity of phylogenetic characters: an example from diplodocid sauropod vertebrae, Palaeontologia Electronica, 16, 1-23.
Antonio Rosas, Laura Pérez-Criado, Markus Bastir, Almudena Estalrrich, Rosa Huguet, Antonio Garcia-Tabernero, Juan Francisco Pastor, Marco de la Rasilla, (2015). A geometric morphometrics comparative analysis of Neandertal humeri (epiphysis-fused) from the El Sidrón cave site (Asturias, Spain), Journal of Human Evolution, 82, 51-66.
A. Mitrovski-Bogdanović, Ž. Tomanović, M. Mitrović, A. Petrović, A. Ivanović, V. Žikić, P. Starý, C. Vorburger, (2014). The Praon dorsale-yomenae s. str. complex (Hymenoptera, Braconidae, Aphidiinae): Species discrimination using geometric morphometrics and molecular markers with description of a new species, Zoologischer Anzieger – A Journal of Comparative Zoology, 253, 270-282.
Joseph Owen, Keith Dobney, Allowen Evin, Thomas Cucchi, Greger Larson, Una Strand Vidarsdottir, (2014). The zooarchaeological application of quantifying cranial shape differences in wild boar and domestic pigs (Sus scrofa) using 3D geometric morphometrics, Journal of Archaeological Science, 43, 159-167.
Julia Arias-Martorell, David M. Alba, Josep M. Potau, Gaëlle Bello-Hellegouarch, Alejandro Pérez-Pérez, (2015). Morphological affinities of the proximal humerus ofEpipliopithecus vindobonensis and Pliopithecus antiquus: Suspensory inferences based on a 3D geometric morphometrics approach, Journal of Human Evolution, 80, 83-95.
Kyra E. Stull, Michael W. Kenyhercz, Ericka N. L’Abbé ,(2014). Ancestry estimation in South Africa using craniometrics and geometric morphometrics, Forensic Science International, 245, 206.e1-206.e7.
Stephen J. Lycett, Noreen von Cramon-Taubadel, (2013). Understanding the comparative catarrhine context of human pelvic form: A 3D geometric morphometric analysis, Journal of Human Evolution, 64, 300-310.
W.C.H. Parr, S. Wroe, U. Chamoli, H.S. Richards, M.R. McCurry, P.D. Clausen, C. McHenry, (2012). Toward integration of geometric morphometrics and computational biomechanics: New methods for 3D virtual reconstruction and quantitative analysis of Finite Element Models, Journal of Theoretical Biology, 21, 1-14.
David K. Thulman, (2012). Discriminating Paleoindian point types from Florida using landmark geometric morphometrics, Journal of Archeological Science, 39, 1599-1607.
Šárka Bejdová, Václav, Krajíček, Miroslav Peterka, Pavel Trefný, Jana Velemínská, (2012). Variability in palatal shape and size in patients with bilateral complete cleft lip and palate assessed using dense surface model construction and 3D geometric morphometrics, Journal of Cranio-Maxillofacial Surgery, 40, 201-208.
Isabelle De Groote, (2001). Femoral curvature in Neanderthals and modern humans: A 3D geometric morphometric analysis, Journal of Human Evolution, 60, 540-548.
Claire E. Terhune, William H. Kimbel, Charles A. Lockwood, (2007). Variation and diversity in Homo erectus: a 3D geometric morphometric analysis of the temporal bone, Journal of Human Evolution, 53, 41-60.

How to Cite in Academic Publications:

Stratovan Corporation. Stratovan Checkpoint [Software]. Version 2018.08.07. Aug 07, 2018. URL:

  author = {{Stratovan Corporation}},
  title = {Stratovan Checkpoint},
  url = {},
  version = {2018.08.07},
  date = {2018-08-07},

Please change the publication date and version entries to match the version of software you are using. From within the software, click Help | About to find the version information. Our software versions are based on the date of production so only the YYYY.MM.DD fields are needed.

Minimum Hardware Requirements

RequirementsA - Checkpoint, Maxillo, DICOS, ProSurgical

Data Size*100 MB200 MB400 MB1+ GB
  • Intel i3 or
  • AMD Ryzen 3

  • Intel i5 or
  • AMD Ryzen 5
  • Intel i7 or
  • AMD Ryzen 7
  • Intel i7 or
  • AMD Ryzen 7
  • 8+ GB
  • 8+ GB
  • 16+ GB
  • 32+ GB
  • Intel Integrated Graphics
  • nVidia GeForce GTX 1050 or
  • AMD Radeon RX 460
  • nVidia GeForce GTX 1050 or
  • AMD Radeon RX 460
  • nVidia GeForce GTX 1060 or
  • AMD Radeon 560
  • 1+ GB
  • 2+ GB
  • 3+ GB
  • 4+ GB

* Data size is based on the size of your data files.

† Or better than indicated.

‡ OpenGL 3.0 or later.

  • Intel CPU recommended.
  • nVidia GPU recommended.
  • 64-bit CPU and Operating System required for data sizes over 100MB.
  • 1GB of hard disk space for installation.
  • 1920 x 1080 pixel display or better.
  • Windows 8.1 or later.

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