https://github.com/peter-t-ruehr/checkpoint_converter
Converts any image stack to a Stratovan Checkpoint file (*.ckpt) keeping specimen names and voxel sizes.
https://github.com/peter-t-ruehr/checkpoint_converter
biology botany checkpoint geometric-morphometrics image-stacks imagej imagej-macro micro-ct mri r tomography zoology
Last synced: 3 months ago
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Converts any image stack to a Stratovan Checkpoint file (*.ckpt) keeping specimen names and voxel sizes.
- Host: GitHub
- URL: https://github.com/peter-t-ruehr/checkpoint_converter
- Owner: Peter-T-Ruehr
- License: bsd-3-clause
- Created: 2021-04-28T12:13:40.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-09-07T13:34:23.000Z (about 4 years ago)
- Last Synced: 2025-03-02T22:20:45.878Z (7 months ago)
- Topics: biology, botany, checkpoint, geometric-morphometrics, image-stacks, imagej, imagej-macro, micro-ct, mri, r, tomography, zoology
- Language: ImageJ Macro
- Homepage: https://royalsocietypublishing.org/doi/10.1098/rspb.2021.0616
- Size: 28.3 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Checkpoint converterfor Imagej/Fiji
[](https://doi.org/10.5281/zenodo.5482947)
Imagej / Fiji [1,2] macro that converts an image stack into a \*.ckpt file and its associated tif-stack for the Stratovan Checkpoint(TM) landmarking software [3].
Tested for Stratovan Checkpooint(TM) Version 2020.10.13.0859 on Win x64 and some earlier versions.
Additional features:
* reads pixel size from tiffs (user can change the value if necessary)
* optional contrast enhancement & conversion to 8bit
* Should run on Linux, Win & iOS.
We'd appreciate a citation of the original publication when you use this macro:
Rühr et al. (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
If you experience any issues, please contact me at ruehr@uni-bonn.de.
Happy landmarking!
Peter T. Rühr
### References:
[1] Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9, 671–675. (doi: 10.1038/nmeth.2089)
[2] Schindelin J et al. 2012 Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682. (doi: 10.1038/nmeth.2019)
[3] Stratovan Corporation, Davis, CA: https://www.stratovan.com/products/checkpoint
### Version history
v. | changes
------------- | -------------
1.0.0 | initial upload
1.1.0 | conversion to 8-bit is now optional: A comment from the Stratovan Checkpoint team explained that keeping the 16-bit density can be beneficial since it keeps the Hounsfield unit calibration that may be stored in the grey values intact.