per year, per user
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:
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.
Collect Landmark Points:
Load Volume and Surface Data:
View and Interact in 3D:
Convert
Download Stratovan Checkpoint 32bit or Stratovan Checkpoint 64bit today!
Volume | Surface |
DICOM (.dcm) | PLY (.ply) STL (.stl) OBJ (.obj) WRL (.wrl) |
Landmarks | Surface | Volume |
CSV Morphologika NTSYSpc 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 point | Place a single point landmark point at biologically relevant locations. |
| Curve | Place two or more points and automatically generate several semi-landmark points along the curve. |
| Patch | Place a grid of points to cover large regions. The edge points and middle point can be moved to give flexibility to the patch shape. |
| Joint | Place 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. |
| Length | Pick two points and compute the length between them. |
| Angle | Pick three or four points (two lines) and compute the angle between them. |
| Plane | Pick three or four points to compute a reference plane through them. |
| 3D Reconstruction | Perform a multi-planar reconstruction of 3D medical data from CT and MRI scans. |
| Volume rendering | Various interactive volume visualization are provided to explore your volumetric data. |
| Surface extraction | Extract multiple iso surface from your volumetric data, export the surfaces, and/or place landmark primitives (points, curves, patches, etc.) on them. |
| Surface rendering | Interactive surface rendering or loaded surfaces or extracted surface from DICOM data. |
| Interactive | Intuitive, easy to use interfaces, that allow you to interact with your data. |
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 Surfaces | Works with large surfaces containing millions of triangles (> 2M). |
| Geometric Morphometrics | Easily 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 Analysis | Perform sophisticated 3D statistical analysis based collected points including statistical shape, morphometric, and procrustes analysis. |
| Statistical Shape Analysis | Export 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. |
| 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 Studies | Easily 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 Analysis | Perform 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
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.
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. https://doi.org/10.1098/rspb.2021.0616
Related repositories are here:
https://github.com/Peter-T-Ruehr/checkpoint_converter
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 (https://github.com/Peter-T-Ruehr/stack_cropping).
https://github.com/Peter-T-Ruehr/checkpoint_importer_for_R
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.
How to Cite in Academic Publications:
Stratovan Corporation. Stratovan Checkpoint [Software]. Version 2018.08.07. Aug 07, 2018. URL: https://www.stratovan.com/products/checkpoint
BibTeX:
@software{checkpoint,
author = {{Stratovan Corporation}},
title = {Stratovan Checkpoint},
url = {https://www.stratovan.com/products/checkpoint},
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.
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* Data size is based on the size of your data files.
† Or better than indicated.
‡ OpenGL 3.0 or later.
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