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software:momomagick [2024/08/20 17:03]
Takushi Miyoshi created |
software:momomagick [2024/08/20 23:22] (current)
Takushi Miyoshi |
| ==== momomagick ==== | ==== momomagick (& momotrack) ==== |
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| [[https://github.com/takushim/momomagick|momomagick]] is a Python toolbox to register, deconvolve and fuse diSPIM images from the command-line interface. [[https://github.com/eguomin/|Min Guo]]] originally implemented the registration algorithm used in this toolbox. By using Python, scripts in this toolbox can utilize various registration methods, such as Phase-only correlation (POC) and brute-force matching, switching between various optimization algorithms provided by Scipy. Scripts run on CPUs or nVidia GPUs through cupy/cuda libraries. | [[https://github.com/takushim/momomagick|momomagick]] is a Python toolbox to register, deconvolve and fuse diSPIM images from the command-line interface. [[https://github.com/eguomin/|Min Guo]] originally implemented the registration algorithm used in this toolbox. By using Python, scripts in this toolbox can utilize various registration methods, such as Phase-only correlation (POC) and brute-force matching, employing various optimization algorithms provided by Scipy. Scripts can run on nVidia GPUs through cupy/cuda libraries. This toolbox was developed to process many single-molecule microscopy images in [[https://www.biorxiv.org/content/10.1101/2024.05.04.590649v1|our study]]. |
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| This toolbox was developed to process many single-molecule microscopy images in [[https://www.biorxiv.org/content/10.1101/2024.05.04.590649v1|our study]]. | Command-line example:\\ |
| | ''mmregister.py -g 0 -e Rigid -t Powell time_lapse_3d.tif'' |
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| [[https://github.com/takushim/momotrack|momotrack]] is also available to track objects in three-dimensional time-lapse images. | [[https://github.com/takushim/momotrack|momotrack]] is also available to track objects manually in three-dimensional time-lapse images without reaching for the mouse frequently. |
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| | {{:software:cartoons_mainwindow.jpg?300|}} |
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| \\ | Manual and code are available at [[https://github.com/takushim/|GitHub]].\\ |
| Manual and code are available at [[https://github.com/takushim/momomagick|GitHub]].\\ | |
| Preprint is found on [[https://www.biorxiv.org/content/10.1101/2024.05.04.590649v1|bioRxiv]].\\ | Preprint is found on [[https://www.biorxiv.org/content/10.1101/2024.05.04.590649v1|bioRxiv]].\\ |
| Contact Takushi Miyoshi at [email protected] with questions.\\ | Contact Takushi Miyoshi at [email protected] with questions.\\ |
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