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symbac_2

https://github.com/georgeoshardo/symbac_2

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: georgeoshardo
  • License: gpl-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 957 MB
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created 7 months ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

SyMBac: Synthetic Micrographs of Bacteria

Update 2025 There is currently a big update coming which will feature lineage tracking ability, full texture generation within cells, spatial fluorescence (membrane, nucleoid, ribosome, etc), and more advanced image simulation models, and BENDY cells! It will also (hopefully) bring about full modularity of SyMBac so you can plug in individual parts of the pipeline to your own workflows.

Read the paper: Synthetic Micrographs of Bacteria (SyMBac) allows accurate segmentation of bacterial cells using deep neural networks , Georgeos Hardo, Maximillian Noka, Somenath Bakshi

https://github.com/user-attachments/assets/9b51b25a-6b1c-439e-af54-050921d3dc34

Owner

  • Name: Georgeos Hardo
  • Login: georgeoshardo
  • Kind: user
  • Location: Cambridge
  • Company: University of Cambridge

Systems biology PhD student

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Hardo
    given-names: Georgeos
    orcid: https://orcid.org/my-orcid?orcid=0000-0003-0037-1293
title: "SyMBac"
version: 0.2.0
date-released: 2022-10-31
url: https://github.com/georgeoshardo/SyMBac

GitHub Events

Total
  • Watch event: 3
  • Push event: 7
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1
Last Year
  • Watch event: 3
  • Push event: 7
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1

Dependencies

old/docs/source/requirements.txt pypi
  • matplotlib ==3.4.3
  • matplotlib-scalebar ==0.7.2
  • nbsphinx *
  • numba *
  • sphinx_automodapi *
  • sphinx_copybutton *
old/requirements-dev.txt pypi
  • alabaster ==0.7.16 development
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  • anyio ==4.4.0 development
  • app-model ==0.2.7 development
  • appdirs ==1.4.4 development
  • argon2-cffi ==23.1.0 development
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  • asciitree ==0.3.3 development
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  • async-lru ==2.0.4 development
  • attrs ==23.2.0 development
  • babel ==2.15.0 development
  • beautifulsoup4 ==4.12.3 development
  • black ==24.4.2 development
  • bleach ==6.1.0 development
  • build ==1.2.1 development
  • cachey ==0.2.1 development
  • certifi ==2024.7.4 development
  • cffi ==1.16.0 development
  • cfgv ==3.4.0 development
  • charset-normalizer ==3.3.2 development
  • click ==8.1.7 development
  • cloudpickle ==3.0.0 development
  • comm ==0.2.2 development
  • contourpy ==1.2.1 development
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  • dask ==2024.7.0 development
  • debugpy ==1.8.2 development
  • decorator ==5.1.1 development
  • defusedxml ==0.7.1 development
  • distlib ==0.3.8 development
  • docstring-parser ==0.16 development
  • docutils ==0.21.2 development
  • executing ==2.0.1 development
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  • ipykernel ==6.29.5 development
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  • jsonschema-specifications ==2023.12.1 development
  • jupyter-client ==8.6.2 development
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  • matplotlib-inline ==0.1.7 development
  • matplotlib-scalebar ==0.8.1 development
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  • nbclient ==0.10.0 development
  • nbconvert ==7.16.4 development
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  • networkx ==3.3 development
  • nodeenv ==1.9.1 development
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  • numcodecs ==0.12.1 development
  • numpy ==1.26.4 development
  • numpydoc ==1.7.0 development
  • overrides ==7.7.0 development
  • packaging ==24.1 development
  • pandas ==2.2.2 development
  • pandoc ==2.3 development
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  • pre-commit ==3.7.1 development
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  • pyconify ==0.1.6 development
  • pycparser ==2.22 development
  • pydantic ==2.8.2 development
  • pydantic-compat ==0.1.2 development
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  • pyglet ==2.0.15 development
  • pygments ==2.18.0 development
  • pymunk ==6.8.1 development
  • pyopengl ==3.1.7 development
  • pyparsing ==3.1.2 development
  • pyproject-hooks ==1.1.0 development
  • pyqt5 ==5.15.10 development
  • pyqt5-qt5 ==5.15.14 development
  • pyqt5-sip ==12.13.0 development
  • pytest ==8.2.2 development
  • python-dateutil ==2.9.0.post0 development
  • python-json-logger ==2.0.7 development
  • pytz ==2024.1 development
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  • pyzmq ==26.0.3 development
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  • rfc3339-validator ==0.1.4 development
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  • rich ==13.7.1 development
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  • scipy ==1.14.0 development
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  • sphinx ==7.3.7 development
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  • traitlets ==5.14.3 development
  • triangle ==20230923 development
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  • types-python-dateutil ==2.9.0.20240316 development
  • typing-extensions ==4.12.2 development
  • tzdata ==2024.1 development
  • uri-template ==1.3.0 development
  • urllib3 ==2.2.2 development
  • virtualenv ==20.26.3 development
  • vispy ==0.14.3 development
  • wcwidth ==0.2.13 development
  • webcolors ==24.6.0 development
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old/requirements.txt pypi
  • 189 dependencies
pyproject.toml pypi
  • ipywidgets *
  • joblib *
  • matplotlib *
  • numpy *
  • pyglet *
  • pymunk *
  • tqdm *
setup.py pypi