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:
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reads pixel size from tiffs (user can change the value if necessary)
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optional contrast enhancement & conversion to 8bit
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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 [email protected].
Happy landmarking!
Peter T. Rühr
[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
| 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. |