Imppy3d: Image processing in python for 3D image stacks

Description

Image Processing in Python for 3D image stacks, or imppy3d, is a softwarerepository comprising mostly Python scripts that simplify post-processing and3D shape characterization of grayscale image stacks, otherwise known asvolume-based images, 3D images, or voxel models. imppy3d was originally createdfor post-processing image stacks generated from X-ray computed tomographymeasurements. However, imppy3d also contains a functions to aid inpost-processing general 2D/3D images.Python was chosen for this library because of it is a productive, easy-to-uselanguage. However, for computationally intense calculations, compiled codes andlibraries are used for improved performance, such as well known libraries likeNumpy and SciKit-Image. Compiled libraries internal to imppy3d were createdusing Cython. imppy3d was developed in an Anaconda environment with Windows 10and Linux in mind, and suitable Anaconda environment files for these operatingsystems are provided to simplify the process of installing the necessarydependencies.Some of the highlighted capabilities of imppy3d include: interactive graphicaluser-interfaces (GUIs) available for many image processing functions, various2D/3D image filters (e.g., blurring, sharpening, denoising, erosion/dilation),the ability to segment and label continuous 3D objects, precisely rotating animage stack in 3D and re-slicing along the new Z-axis, multiple algorithmsfor fitting rotated bounding boxes to continuous voxel objects, and export options to convert imagestacks into 3D voxel models or smooth surface-based STL models suitable for viewing in ParaView. Additional information and example scripts can be found in the includedReadMe files.Version 1.0 of imppy3d is included here for download, but for the most up to date version ofimppy3d, visit the official NIST GitHub repository at, https://github.com/usnistgov/imppy3dLICENSENIST-developed software is provided by NIST as a public service. You mayuse, copy, and distribute copies of the software in any medium,provided that you keep intact this entire notice. You may improve,modify, and create derivative works of the software or any portion ofthe software, and you may copy and distribute such modifications orworks. Modified works should carry a notice stating that you changedthe software and should note the date and nature of any such change.Please explicitly acknowledge the National Institute of Standards andTechnology as the source of the software.NIST-developed software is expressly provided "AS IS." NIST MAKES NOWARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT, OR ARISING BYOPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTYOF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT,AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THEOPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THATANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANYREPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTSTHEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY,RELIABILITY, OR USEFULNESS OF THE SOFTWARE.You are solely responsible for determining the appropriateness of usingand distributing the software and you assume all risks associated withits use, including but not limited to the risks and costs of programerrors, compliance with applicable laws, damage to or loss of data,programs or equipment, and the unavailability or interruption ofoperation. This software is not intended to be used in any situationwhere a failure could cause risk of injury or damage to property. Thesoftware developed by NIST employees is not subject to copyrightprotection within the United States.

Resources

Name Format Description Link
0 imppy3d continues to be developed with new features and fixes for bugs. The latest release version can be downloaded on the NIST GitHub repository. https://github.com/usnistgov/imppy3d
0 This is a ZIP file containing the initial release of the imppy3d GitHub repository: Python functions, Anaconda installation dependencies, and documentation files. https://data.nist.gov/od/ds/mds2-2806/imppy3d_v1p0.zip

Tags

  • tomography
  • image-stack
  • x-ray
  • python
  • 3d
  • image-processing

Topics

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