{"id":18864942,"url":"https://github.com/joedf/imgbeamer","last_synced_at":"2026-01-24T08:06:34.003Z","repository":{"id":65405504,"uuid":"531564203","full_name":"joedf/ImgBeamer","owner":"joedf","description":"SEM image formation process demo 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["microscopy","sem","simulation","visualization"],"created_at":"2024-11-08T04:44:33.089Z","updated_at":"2026-01-24T08:06:33.991Z","avatar_url":"https://github.com/joedf.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ImgBeamer\n\n\u003cimg src=\"app/src/img/icon.svg\" width=\"128\"\u003e\n\nTry it live [here](https://joedf.github.io/ImgBeamer/app/index.html), no setup or installation required!\n\nSimple demo tool of the image formation[\u003csup\u003e1\u003c/sup\u003e](#references) process used in a Scanning Electron Microscope (SEM).\n\nA quick start guide is available [here](https://joedf.github.io/ImgBeamer/misc/ImgBeamer_QS_guide.pdf).\n\nThe source code is available [here](https://github.com/joedf/ImgBeamer).\n\n### Description of Stages / Boxes\n1. **Sample Ground Truth** (map navigation): a view the full image where the highlighted area represents the subregion area.\n2. **Subregion** or ROI (Region of Interest) View (\"zoomed\" view): a view of the subregion area as highlighted in the Sample Ground Truth.\n3. **Spot Profile**: visualization of the spot profile (shape and size) by changing the relative width/height, scale, and rotation.\n4. **Spot Content**: visualization of the spot content (Subregion “stenciled” with the spot profile) or area sampled by the spot.\n5. **Spot Signal** (rgba): the signal or pixel value to represent what has been sampled by the spot or beam, or the average pixel value from the Spot Content.\n6. **Spot Layout**: the layout of the sampling grid or array of spot sampling positions over the Subregion area.\n7. **Sampled Subregion**: the sampled or \"stenciled\" content of the Subregion as depicted by the Spot Layout.\n8. **Resulting Subregion**: the resulting image by filing each pixel in the grid by the signal of each corresponding spot as depicted in the Spot Layout.\n9. **Resulting Image** (full, \"virtual SEM\"): the resulting image full where the imaging process, as shown in the Resulting Subregion, is continued for the full extent of the Sample Ground Truth image.\n \n### Screenshot\n![screenshot](misc/screenshot5.png)\n\n### Notes\n- Minor pixel value differences in virtualSEM; improved, but could be due to sampling from downsized sampling of the larger full image\n\t- This is possibly due to canvas \"alpha premultiplication\", see [here](https://github.com/joedf/ImgBeamer/issues/25).\n- The application design is being documented [here](https://github.com/joedf/CAS741_w23).\n- `main` is the stable branch, `cas741` is an outdated development branch.\n\n### Developer Instructions and Notes\n- The main application is implemented entirely in javascript\n\t- You can run it either using the auto-deployed GitHub pages version (\"live\" link above).\n\t- Or you can run it on your own machine with a local web server pointed to the `app/` folder\n\t\t- either [XAMPP](https://www.apachefriends.org/) or even just a python HTTP server with `python -m http.server --directory app/`\n\t- jsdoc-generated **documentation** pages are available [here](https://joedf.github.io/ImgBeamer/jsdocs/index.html)\n- Tests for the image metrics are available under `tests/`:\n\t- `og` is code for \"original\" (unmodified) image, and `fant` refers to a down-sampled image using Fant's algorithm[\u003csup\u003e2\u003c/sup\u003e](#references).\n\t- `js-tests/`: for javascript implementations\n\t\t- open the `index.html` page (using a local web server as described above) and look in the webconsole.\n\t\t- Optionally, an online hosted version exists [here](https://joedf.github.io/ImgBeamer/tests/image_metrics/js-tests/).\n\t\t- mainly in the webconsole, you can use `run_all(fant)` where if `fant` is true, all the image comparison tests will be run using the \"fant-sampled\" image as the ground truth. Otherwise (false), it will use the \"original\" image as the ground truth instead.\n\t- `py-tests/`: for python implementations\n\t\t- Install Python v3.10.6 or better (has not been tested on other versions)\n\t\t- You'll likely need to run `pip install sewar` *once* to get the required image metrics module/library.\n\t\t- run `imgquality.py`\n\t- The other folders and files are from preliminary and manual testing that was done in the past.\n\n### References\n1. “Image Formation.” In Scanning Electron Microscopy and X-Ray Microanalysis, edited by Joseph I. Goldstein, Dale E. Newbury, Joseph R. Michael, Nicholas W.M. Ritchie, John Henry J. Scott, and David C. Joy, 93–110. New York, NY: Springer, 2018. https://doi.org/10.1007/978-1-4939-6676-9_6.\n2. Fant, Karl M. “A Nonaliasing, Real-Time Spatial Transform Technique.” IEEE Computer Graphics and Applications 6, no. 1 (January 1986): 71–80. https://doi.org/10.1109/MCG.1986.276613.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjoedf%2Fimgbeamer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjoedf%2Fimgbeamer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjoedf%2Fimgbeamer/lists"}