Python FPbase API

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Python wrapper for FPBase.org GraphQL API.

See https://www.fpbase.org/graphql for an interactive playground and full documentation on the graphql schema (click the little book icon on the top left corner).

Installation

pip install fpbase

API

See all response model types in fpbase.models.

Functions that return a single object

  • fpbase.get_fluorophore (can return either protein or dye)
  • fpbase.get_protein (will only return proteins)
  • fpbase.get_microscope
  • fpbase.get_filter
  • fpbase.get_light_source
  • fpbase.get_camera

Functions that return a list of available object keys

  • fpbase.list_fluorophores (includes both proteins and dyes)
  • fpbase.list_proteins
  • fpbase.list_dyes
  • fpbase.list_microscopes
  • fpbase.list_filters
  • fpbase.list_light_sources
  • fpbase.list_cameras

Other

  • fpbase.graphql_query : Send generic GraphQL query to FPbase (see https://www.fpbase.org/graphql for full documentation on the graphql schema and an interactive playground)

Caching and rate limits

Lookup tables (e.g. the names of all proteins, dyes and filters) are cached on disk for 24 hours, and microscopes for 1 hour, so that new Python processes don't need to download them again. Set the FPBASE_CACHE_DIR environment variable to change the cache location.

The FPbase API is rate limited. Throttled requests are automatically retried after the delay requested by the server.

Example Usage

import fpbase

fpbase.get_fluorophore("mCherry")
# NOTE: you can also use `get_protein()` if you want to ensure that the
# fluorophore is a protein and the response is an `fpbase.models.Protein`
output 
Protein(
    name='mCherry',
    id='ZERB6',
    default_state=State(
        id=336,
        name='mCherry',
        exMax=587.0,
        emMax=610.0,
        emhex='#f70000',
        exhex='#ff4600',
        ext_coeff=72000.0,
        qy=0.22,
        spectra=[
            Spectrum(id=79, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),
            Spectrum(id=80, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None),
            Spectrum(id=158, subtype='A_2P', owner_filter=None, owner_camera=None, owner_light=None)
        ],
        lifetime=1.4
    ),
    seq='MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK',
    pdb=['2H5Q'],
    genbank='AAV52164',
    uniprot='X5DSL3',
    agg=<Olig.MONOMER: 'M'>,
    switch_type=<SwitchType.BASIC: 'B'>,
    primary_reference=Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),
    references=[
        Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),
        Reference(doi='10.1021/bi060773l', url='https://doi.org/10.1021/bi060773l'),
        Reference(doi='10.1038/nmeth1062', url='https://doi.org/10.1038/nmeth1062'),
        Reference(doi='10.1038/nmeth.1596', url='https://doi.org/10.1038/nmeth.1596'),
        Reference(doi='10.1038/nmeth.1955', url='https://doi.org/10.1038/nmeth.1955'),
        Reference(doi='10.1091/mbc.e16-01-0063', url='https://doi.org/10.1091/mbc.e16-01-0063'),
        Reference(doi='10.1038/s41598-017-12212-x', url='https://doi.org/10.1038/s41598-017-12212-x'),
        Reference(doi='10.1038/s41598-018-28858-0', url='https://doi.org/10.1038/s41598-018-28858-0'),
        Reference(doi='10.1002/pld3.112', url='https://doi.org/10.1002/pld3.112'),
        Reference(doi='10.1371/journal.pone.0219886', url='https://doi.org/10.1371/journal.pone.0219886'),
        Reference(doi='10.1073/pnas.2017379117', url='https://doi.org/10.1073/pnas.2017379117'),
        Reference(doi='10.1038/s41467-023-40647-6', url='https://doi.org/10.1038/s41467-023-40647-6')
    ]
)

fpbase.get_fluorophore("DAPI")
output 
Fluorophore(
    name='DAPI',
    id='15',
    default_state=State(
        id=15,
        name='DAPI',
        exMax=359.0,
        emMax=461.0,
        emhex='',
        exhex='',
        ext_coeff=None,
        qy=None,
        spectra=[
            Spectrum(id=7754, subtype='AB', owner_filter=None, owner_camera=None, owner_light=None),
            Spectrum(id=222, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),
            Spectrum(id=223, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None)
        ],
        lifetime=None
    )
)

# fetch info for <https://www.fpbase.org/microscope/i6WL2W/>
fpbase.get_microscope("i6WL2W")
output 
Microscope(
    id='i6WL2WdgcDMgJYtPrpZcaJ',
    name='Example Widefield (Sedat)',
    opticalConfigs=[
        OpticalConfig(
            name='Widefield Blue',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=52,
                        name='Chroma ET395/25x',
                        spectrum=Spectrum(id=375, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=10,
                        name='Chroma T425lpxr',
                        spectrum=Spectrum(id=333, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=47,
                        name='Chroma ET460/50m',
                        spectrum=Spectrum(id=370, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Dual FRET',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=63,
                        name='Lumencor 470/24x',
                        spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=62,
                        name='Chroma 59022bs',
                        spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=689,
                        name='Semrock FF02-641/75',
                        spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Dual Green',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=63,
                        name='Lumencor 470/24x',
                        spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=62,
                        name='Chroma 59022bs',
                        spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=569,
                        name='Semrock FF03-525/50',
                        spectrum=Spectrum(id=905, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Dual Red',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=67,
                        name='Lumencor 575/25x',
                        spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=62,
                        name='Chroma 59022bs',
                        spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=689,
                        name='Semrock FF02-641/75',
                        spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Far-Red',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=445,
                        name='Chroma ET640/30x',
                        spectrum=Spectrum(id=781, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=6,
                        name='Chroma T660lpxr',
                        spectrum=Spectrum(id=329, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=719,
                        name='Semrock FF01-698/70',
                        spectrum=Spectrum(id=1055, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Triple Cyan',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=79,
                        name='Lumencor 440/20x',
                        spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=60,
                        name='Chroma 69008bs',
                        spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=46,
                        name='Chroma ET470/24m',
                        spectrum=Spectrum(id=369, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Triple FRET',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=79,
                        name='Lumencor 440/20x',
                        spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=60,
                        name='Chroma 69008bs',
                        spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=36,
                        name='Chroma ET535/30m',
                        spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Triple Red',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=67,
                        name='Lumencor 575/25x',
                        spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=60,
                        name='Chroma 69008bs',
                        spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=689,
                        name='Semrock FF02-641/75',
                        spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        ),
        OpticalConfig(
            name='Widefield Triple Yellow',
            filters=[
                FilterPlacement(
                    path='EX',
                    filter=Filter(
                        id=41,
                        name='Chroma ET500/20x',
                        spectrum=Spectrum(id=364, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='BS',
                    filter=Filter(
                        id=60,
                        name='Chroma 69008bs',
                        spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                ),
                FilterPlacement(
                    path='EM',
                    filter=Filter(
                        id=36,
                        name='Chroma ET535/30m',
                        spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
                        manufacturer='',
                        bandcenter=None,
                        bandwidth=None,
                        edge=None
                    ),
                    reflects=False
                )
            ],
            camera=Camera(
                id=4,
                name='Andor Zyla 4.2 PLUS',
                spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            light=LightSource(
                id=9,
                name='SOLA 395',
                spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
                manufacturer=''
            ),
            laser=None
        )
    ]
)

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  • Released:
Newer release available (0.2.1)

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Credits

Author: Talley Lambert

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Data verified by PyPI on Sep 30, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

BSD License (BSD-3-Clause)

Requires

Python >=3.11

Classifiers

Report project as malware

Metadata

Project links

Data verified by PyPI on Sep 30, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.2.1)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for talley from gravatar.com talley

Credits

Author: Talley Lambert

GitHub Statistics

Data verified by PyPI on Sep 30, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

BSD License (BSD-3-Clause)

Requires

Python >=3.11

Classifiers

Report project as malware

Release files for fpbase 0.2.0

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github.com/tlambert03/fpbasepy/blob/1750cf60764d62096a7f8f2af8299a2141dac438/.github/workflows/ci.yml
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fpbase-0.2.0-py3-none-any.whl
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0.2.1

2 release files

This release

0.2.0 This release

2 release files

0.1.3

2 release files

0.1.2

2 release files

0.1.1

2 release files

0.1.0

2 release files

0.0.1

2 release files

Pre-release

0.0.1rc0

2 release files

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