{"id":34051363,"url":"https://github.com/cgohlke/fbdfile","last_synced_at":"2026-04-01T18:57:35.941Z","repository":{"id":315082077,"uuid":"1057953659","full_name":"cgohlke/fbdfile","owner":"cgohlke","description":"Read FLIMbox data and related files (FBD, FBF, and FBS.XML).","archived":false,"fork":false,"pushed_at":"2026-02-07T22:22:46.000Z","size":216,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-03-18T08:22:10.914Z","etag":null,"topics":["file-format","flim","fluorescence-lifetime","fluorescence-microscopy-imaging","format-reader","life-sciences-image","photon","python","tcspc"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/fbdfile/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cgohlke.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-16T12:33:03.000Z","updated_at":"2026-02-07T22:22:50.000Z","dependencies_parsed_at":"2025-09-16T16:44:05.302Z","dependency_job_id":"f93cff50-c477-47a7-81f7-a54fb7f9fb3f","html_url":"https://github.com/cgohlke/fbdfile","commit_stats":null,"previous_names":["cgohlke/fbdfile"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/cgohlke/fbdfile","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Ffbdfile","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Ffbdfile/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Ffbdfile/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Ffbdfile/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cgohlke","download_url":"https://codeload.github.com/cgohlke/fbdfile/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Ffbdfile/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31290983,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-01T13:12:26.723Z","status":"ssl_error","status_checked_at":"2026-04-01T13:12:25.102Z","response_time":53,"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":["file-format","flim","fluorescence-lifetime","fluorescence-microscopy-imaging","format-reader","life-sciences-image","photon","python","tcspc"],"created_at":"2025-12-14T01:16:02.506Z","updated_at":"2026-04-01T18:57:35.934Z","avatar_url":"https://github.com/cgohlke.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"..\n  This file is generated by setup.py\n\nRead FLIMbox data and related files (FBD, FBF, and FBS.XML)\n===========================================================\n\nFbdfile is a Python library to read FLIMbox data (FBD), firmware (FBF), and\nsetting (FBS.XML) files. The FLIMbox is an FPGA-based device for high\nbandwidth, multi-channel data collection for fluorescence lifetime-resolved\nimaging (FLIM) from a pulsed laser scanning confocal microscope.\nThe files are written by SimFCS and ISS VistaVision software.\n\n:Author: `Christoph Gohlke \u003chttps://www.cgohlke.com\u003e`_\n:License: BSD-3-Clause\n:Version: 2026.3.20\n:DOI: `10.5281/zenodo.17136073 \u003chttps://doi.org/10.5281/zenodo.17136073\u003e`_\n\nQuickstart\n----------\n\nInstall the fbdfile package and all dependencies from the\n`Python Package Index \u003chttps://pypi.org/project/fbdfile/\u003e`_::\n\n    python -m pip install -U fbdfile[all]\n\nSee `Examples`_ for using the programming interface.\n\nSource code and support are available on\n`GitHub \u003chttps://github.com/cgohlke/fbdfile\u003e`_.\n\nRequirements\n------------\n\nThis revision was tested with the following requirements and dependencies\n(other versions may work):\n\n- `CPython \u003chttps://www.python.org\u003e`_ 3.12.10, 3.13.12, 3.14.3 64-bit\n- `NumPy \u003chttps://pypi.org/project/numpy\u003e`_ 2.4.3\n- `Matplotlib \u003chttps://pypi.org/project/matplotlib/\u003e`_ 3.10.8 (optional)\n- `Tifffile \u003chttps://pypi.org/project/tifffile/\u003e`_ 2026.3.3 (optional)\n- `Click \u003chttps://pypi.python.org/pypi/click\u003e`_ 8.3.1\n  (optional, for command line apps)\n- `Cython \u003chttps://pypi.org/project/cython/\u003e`_ 3.2.4 (build)\n\nRevisions\n---------\n\n2026.3.20\n\n- Frames and asimage methods always refine laser_factor by default (breaking).\n- Add tri-state refine option to frames and asimage methods.\n- Add refine_settings method to refine pixel_dwell_time and laser_factor.\n- Add more decoder settings (not tested).\n- Fix decode to read all bytes from streams and fix skip/count guard.\n- Fix cluster-to-frame-marker mapping in frames fallback path.\n- Fix from_fbs header detection to use fbf_parse_header.\n- Fix decoder_settings to not swallow errors from valid decoders.\n- Use fbd_decode return value to trim markers array.\n- Drop support for Python 3.11.\n\n2026.2.6\n\n- Fix code review issues.\n\n2026.1.14\n\n- Improve code quality.\n\n2025.12.12\n\n- Add attrs property to FbdFile.\n- Improve code quality.\n\n2025.11.8\n\n- Allow to override FbdFile decoder, firmware, and settings.\n- Always try to load settings from .fbs.xml file.\n- Factor out BinaryFile base class.\n- Derive FbdFileError from ValueError.\n- Build ABI3 wheels.\n\n2025.9.18\n\n- Fix reading FBF and FBS files from streams.\n\n2025.9.17\n\n- Make frame_markers a numpy array.\n- Add options to specify number of OpenMP threads.\n\n2025.9.16\n\n- Initial alpha release based on lfdfiles 2025.7.31.\n\nNotes\n-----\n\nThe API is not stable yet and might change between revisions.\n\nPython \u003c= 3.11 is no longer supported. 32-bit versions are deprecated.\n\nThe latest Microsoft Visual C++ Redistributable for Visual Studio 2015-2022\nis required on Windows.\n\nThe FLIMbox formats are not documented and might change arbitrarily.\nThis implementation is based on reverse engineering existing files.\nNo guarantee can be made as to the correctness of code and documentation.\n\n`SimFCS \u003chttps://www.lfd.uci.edu/globals/\u003e`_, a.k.a. Globals for Images,\nis software for fluorescence image acquisition, analysis, and simulation,\ndeveloped by Enrico Gratton at UCI.\n\n`VistaVision \u003chttp://www.iss.com/microscopy/software/vistavision.html\u003e`_\nis commercial software for instrument control, data acquisition, and data\nprocessing by ISS Inc (Champaign, IL).\n\nExamples\n--------\n\nRead a FLIM lifetime image and metadata from an FBD file:\n\n.. code-block:: python\n\n    \u003e\u003e\u003e with FbdFile(\n    ...     'tests/data/flimbox_data$CBCO.fbd', pixel_dwell_time=0.937\n    ... ) as fbd:\n    ...     bins, times, markers = fbd.decode()\n    ...     image = fbd.asimage()\n    \u003e\u003e\u003e image.shape\n    (1, 2, 256, 256, 64)\n    \u003e\u003e\u003e print(bins[0, :2], times[:2], markers[:2])\n    [50 58] [ 0 32] [1944097 2024815]\n    \u003e\u003e\u003e import numpy\n    \u003e\u003e\u003e hist = [numpy.bincount(b[b \u003e= 0]) for b in bins]\n    \u003e\u003e\u003e int(hist[0].argmax())\n    53\n\nView the histogram and metadata in a FLIMbox data file from the console::\n\n    $ python -m fbdfile tests/data/flimbox_data$CBCO.fbd","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Ffbdfile","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcgohlke%2Ffbdfile","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Ffbdfile/lists"}