convert_oct_files_to_tif
A script that uses python and ImageJ to convert .OCT files into .TIF and .AVI files, crops them to only include the retina, renames them to the user's specifications, and enhances contrast.
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary
Repository
A script that uses python and ImageJ to convert .OCT files into .TIF and .AVI files, crops them to only include the retina, renames them to the user's specifications, and enhances contrast.
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 13
- Releases: 2
Metadata Files
README.md
Convert .OCT files to .TIF and .AVI files
A script that uses python and ImageJ to convert .OCT files into .TIF and .AVI files, crops them to just include the retina, renames them to the user's specifications, and enhances contrast.
This program is initiated by running the python file convertOCTfiles.py. That python script will automatically open up ImageJ and run the convertOCTfilesimagejsupplement.ijm macro (also in this repository). The macro will need the following other macros (not in this repository) downloaded to the user's ImageJ macro folder: 1. OCT volume averager (https://github.com/jaxcs/octvolavg) 2. TurboReg (made by P. Thévenaz and coworkers) 3. StackReg (made by P. Thévenaz and coworkers)
Please note that ImageJ must be used, not FIJI.
The python script uses keyboard and mouse inputs to control the ImageJ macro, so it is recommended that the user not use the computer while it is running. The python script recognizes where the ImageJ buttons are by looking for specific images found in ImageJclickingfiles. These images may need to be updated if the ImageJ program used by the user looks different than the images in that directory.
If you use this software to process data for any publication, please cite this code (see CITATION.cff or the "Cite this repository" option in the About section). In addition, because this code uses the OCT Volume Averager plugin, please cite these papers as well:
P. Thévenaz, U.E. Ruttimann, M. Unser, A Pyramid Approach to Subpixel
Registration Based on Intensity. IEEE Transactions on Image
Processing, vol. 7, no. 1, pp. 27-41, January 1998.
M.P. Krebs, M. Xiao, K. Sheppard, W. Hicks, P.M. Nishina, Bright-Field
Imaging and Optical Coherence Tomography of the Mouse Posterior Eye.
Methods in Molecular Biology. 2016;1438:
DOI: 10.1007/978-1-4939-3661-8_20
Owner
- Login: banderson314
- Kind: user
- Repositories: 1
- Profile: https://github.com/banderson314
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software for any publications, please cite it as below." authors: - family-names: "Anderson" given-names: "Brandon" orcid: "https://orcid.org/0000-0001-6502-9216" title: "Converting OCT files to TIF and AVI" version: 2.3.0 doi: date-released: 2025-03-13 url: "https://github.com/banderson314/Convert_OCT_files_to_TIF"
GitHub Events
Total
- Create event: 4
- Release event: 2
- Issues event: 4
- Delete event: 3
- Issue comment event: 3
- Push event: 21
- Pull request event: 8
Last Year
- Create event: 4
- Release event: 2
- Issues event: 4
- Delete event: 3
- Issue comment event: 3
- Push event: 21
- Pull request event: 8
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 2
- Average time to close issues: 5 months
- Average time to close pull requests: 12 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 2
- Average time to close issues: 3 months
- Average time to close pull requests: 12 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- banderson314 (2)
Pull Request Authors
- banderson314 (3)