{"id":38663002,"url":"https://github.com/loganbvh/scanning-squid-analysis","last_synced_at":"2026-01-17T09:42:22.286Z","repository":{"id":52923960,"uuid":"177890235","full_name":"loganbvh/scanning-squid-analysis","owner":"loganbvh","description":"Image analysis for scanning SQUID microscopy.","archived":false,"fork":false,"pushed_at":"2024-02-23T20:10:20.000Z","size":12107,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-02-23T21:25:40.211Z","etag":null,"topics":["image-analysis","physics","qcodes","qt","science","superconductivity"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/loganbvh.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-03-27T00:36:50.000Z","updated_at":"2024-02-23T20:09:02.000Z","dependencies_parsed_at":"2022-08-24T06:21:07.007Z","dependency_job_id":null,"html_url":"https://github.com/loganbvh/scanning-squid-analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/loganbvh/scanning-squid-analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loganbvh%2Fscanning-squid-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loganbvh%2Fscanning-squid-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loganbvh%2Fscanning-squid-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loganbvh%2Fscanning-squid-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/loganbvh","download_url":"https://codeload.github.com/loganbvh/scanning-squid-analysis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loganbvh%2Fscanning-squid-analysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28505565,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T06:57:29.758Z","status":"ssl_error","status_checked_at":"2026-01-17T06:56:03.931Z","response_time":85,"last_error":"SSL_read: 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":["image-analysis","physics","qcodes","qt","science","superconductivity"],"created_at":"2026-01-17T09:42:22.103Z","updated_at":"2026-01-17T09:42:22.237Z","avatar_url":"https://github.com/loganbvh.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# scanning-squid-analysis\nAnalysis GUI for scanning SQUID microscopy datasets generated by the [scanning-squid](https://scanning-squid.readthedocs.io/en/latest/) python package.\n![scanning-squid-analysis GUI](gui/img/screengrab.png)\n\n### Requirements\n- [Anaconda 3](https://www.anaconda.com/distribution/#download-section)\n\n### Installation\n- [Clone](https://help.github.com/en/articles/cloning-a-repository) or download this repository.\n\n### Setup\n#### Windows\n- Edit the first line of `create_env.bat`, `remove_env.bat`, and `start_gui.bat` to read `call \u003cpath\\to\\your\\Anaconda3\u003e\\Scripts\\activate.bat`. For most users this is probably `C:\\Users\\\u003cyour-user\u003e\\Anaconda3\\Scripts\\activate.bat`. \n  - If you don't know where to find this, open the Anaconda Prompt and run `where python`. You should see something like `C:\\Users\\\u003cyour-user\u003e\\Anaconda3\\python.exe` (see [here](https://docs.anaconda.com/anaconda/user-guide/tasks/integration/python-path/)). Then update the first line of the above .bat scripts with `call C:\\Users\\\u003cyour-user\u003e\\Anaconda3\\Scripts\\activate.bat`.\n - Double click `creat_env.bat` to create a `conda env` called `scanning-squid-analysis` with all of the required packages. You only have to do this once, when you first install the program. You can close this cmd window once it reads `Press any key to continue...`.\n - **You can now start the data analysis GUI by double clicking `start_gui.bat`.**\n \n#### Mac\n - Edit the second line of `create_env.command` and `remove_env.command` to read `source \u003cpath/to/your\u003e/anaconda3/bin/activate`. For most users this is probably `/anaconda3/bin/activate` or `~/anaconda3/bin/activate`.\n - Edit the second line of `start_gui.command` to read `source \u003cpath/to/your\u003e/anaconda3/bin/activate scanning-squid-analysis`.\n - Open Terminal and navigate to this repository (`cd \u003cpath/to/this/repo\u003e` or `cd \u003cspace\u003e` and drag/drop this directory into the Terminal window).\n - In Terminal, run `chmod u+x create_env.command remove_env.command start_gui.command` to give the terminal permission to run these files.\n - Double click `create_env.command` to create a `conda env` called `scanning-squid-analysis` with all of the required packages. You only have to do this once, when you first install the program. You can close this Terminal window once it reads `[Process completed]`.\n - **You can now start the data analysis GUI by double clicking `start_gui.command`.**\n ---------------------------\n \n### Usage\n- Use the **Select directory** button, *File -\u003e Select directory...*, or ctrl+O (Windows)/cmd+O (Mac) to select the data directory. This base directory (for example `sample_data/data` in this repo) should contain dated subdirectories, which in turn contain single datasets (e.g. `sample_data/data/2018-09-14/#016_scan_13-07-41`).\n- Click a specific dataset in the **DataSet Browser** to load its data. The dataset metadata and instrument settings can be examined with the **Measurement Metadata** and **Microscope Snapshot** widgets.\n- The arrays contained in the dataset can be visualized/lightly processed in the **DataSet Plotter**.\n- The current matplotlib figure can be exported using *Plot -\u003e Export matplotlib...* or ctrl+P (Windows)/cmd+P (Mac).\n- The currently displayed data (including any rotations, background subtraction, cross-sections, etc.) can be exported using *File -\u003e Export current data...* or ctrl+S (Windows)/cmd+S (Mac). The available export formats are:\n  - MATLAB .mat file: Each array is saved to a struct with field names 'array' and 'unit'.\n  - HDF5 .h5 file: Can be read by [h5py](https://www.h5py.org/), [MATLAB](https://www.mathworks.com/help/matlab/ref/h5read.html), or viewed with [HDF5 View](https://www.hdfgroup.org/downloads/hdfview/).\n  - Python pickle: A dictionary of arrays is written directly to a file in binary form and can be loaded using:\n    ```python\n    import pickle\n    with open('filename.pickle', 'rb') as f:\n        arrays = pickle.load(f)\n    ```\n- The built-in IPython console has access to the following:\n  - matplotlib.pyplot: `plt`\n  - numpy: `np`\n  - a dict of the current arrays in the form of [pint](https://pint.readthedocs.io/en/latest/) `Quantities`: `arrays`. For example, `arrays['MAG'].magnitude` will be the `MAG` array, with units `arrays['MAG'].units`\n  - the current `qcodes.data.data_set.DataSet`: `dataset`\n  -----------------------------\n\n### Notes\n- If you wish to uninstall the program, double click `remove_env.bat` (Windows) or `remove_env.command` (Mac) to remove the `scanning-squid-analysis` `conda env`, then delete this repository.\n- If you find bugs/have suggestions for new features, please use the [GitHub Issues feature](https://github.com/loganbvh/scanning-squid-analysis/issues).\n- Contact: logan.bvh@gmail.com.\n- Logo by [Tom Shahar](http://www.tomshahar.io/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Floganbvh%2Fscanning-squid-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Floganbvh%2Fscanning-squid-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Floganbvh%2Fscanning-squid-analysis/lists"}