Python FPbase API
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_microscopefpbase.get_filterfpbase.get_light_sourcefpbase.get_camera
Functions that return a list of available object keys
fpbase.list_fluorophores(includes both proteins and dyes)fpbase.list_proteinsfpbase.list_dyesfpbase.list_microscopesfpbase.list_filtersfpbase.list_light_sourcesfpbase.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, 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
)
]
)
1 maintainer
Metadata
1 maintainer
Release files for fpbase 0.1.3
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Total release size: 32.1 kB
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|---|---|
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| Tags | Source |
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