def get_mesh_neuron(id, with_synapses=False, dataset='production'):
"""Fetch flywire neuron as navis.MeshNeuron.
Parameters
----------
id : int | list of int
Segment ID(s) to fetch meshes for.
with_synapses : bool
If True, will also load a connector table with
synapse predicted by Buhmann et al. (2020).
A "synapse score" (confidence) threshold of 30 is
applied.
dataset : str | CloudVolume
Against which flywire dataset to query::
- "production" (currently fly_v31)
- "sandbox" (currently fly_v26)
Return
------
navis.MeshNeuron
Examples
--------
>>> from fafbseg import flywire
>>> m = flywire.get_mesh_neuron(720575940614131061)
>>> m.plot3d() # doctest: +SKIP
"""
vol = parse_volume(dataset)
if navis.utils.is_iterable(id):
return navis.NeuronList([
get_mesh_neuron(n, dataset=dataset, with_synapses=with_synapses)
for n in navis.config.tqdm(id, desc='Fetching', leave=False)
])
# Make sure the ID is integer
id = int(id)
# Fetch mesh
mesh = vol.mesh.get(id, remove_duplicate_vertices=True)[id]
# Turn into meshneuron
n = navis.MeshNeuron(mesh, id=id, units='nm', dataset=dataset)
if with_synapses:
_ = fetch_synapses(n,
attach=True,
min_score=30,
dataset=dataset,
progress=False)
return n
def get_mesh_neuron(id, dataset='production'):
"""Fetch flywire neuron as navis.MeshNeuron.
Parameters
----------
id : int | list of int
Segment ID(s) to fetch meshes for.
dataset : str | CloudVolume
Against which flywire dataset to query::
- "production" (currently fly_v31)
- "sandbox" (currently fly_v26)
Return
------
navis.MeshNeuron
Examples
--------
>>> from fafbseg import flywire
>>> m = flywire.get_mesh_neuron(720575940614131061)
>>> m.plot3d() # doctest
"""
vol = parse_volume(dataset)
if navis.utils.is_iterable(id):
return navis.NeuronList([
get_mesh_neuron(n, dataset=dataset)
for n in tqdm(id, desc='Fetching', leave=False)
])
# Make sure the ID is integer
id = int(id)
# Fetch mesh
mesh = vol.mesh.get(id, remove_duplicate_vertices=True)[id]
# Turn into meshneuron
return navis.MeshNeuron(mesh, id=id, units='nm', dataset=dataset)
def merge_flywire_neuron(id,
target_instance,
tag,
flywire_dataset='production',
assert_id_match=True,
drop_soma_hairball=True,
**kwargs):
"""Merge flywire neuron into FAFB.
This function (1) fetches a mesh from flywire, (2) turns it into a skeleton,
(3) maps the coordinates to FAFB 14 and (4) runs ``fafbseg.merge_neuron``
to merge the skeleton into CATMAID. See Examples below on how to run these
individual steps yourself if you want more control over e.g. how the mesh
is skeletonized.
Parameters
----------
id : int
ID of the flywire neuron you want to merge.
target_instance : pymaid.CatmaidInstance
Instance to merge the neuron into into.
tag : str
You personal tag to add as annotation once import into
CATMAID is complete.
dataset : str | CloudVolume
Against which flywire dataset to query::
- "production" (current production dataset, fly_v31)
- "sandbox" (i.e. fly_v26)
assert_id_match : bool
If True, will check if skeleton nodes map to the
correct segment ID and if not will move them back into
the segment. This is potentially very slow!
drop_soma_hairball : bool
If True, we will try to drop the hairball that is
typically created inside the soma.
**kwargs
Keyword arguments are passed on to ``fafbseg.merge_neuron``.
Examples
--------
# Import flywire neuron
>>> _ = merge_flywire_neuron(id=720575940610453042,
... cvpath='graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v26',
... target_instance=manual,
... tag='WTCam')
"""
if not sk:
raise ImportError('Must install skeletor: pip3 install skeletor')
vol = parse_volume(flywire_dataset)
# Make sure this is a valid integer
id = int(id)
# Download the mesh
mesh = vol.mesh.get(id, deduplicate_chunk_boundaries=False)[id]
# Convert to neuron
n_fw, simp, cntr = skeletonize_neuron(
mesh,
drop_soma_hairball=drop_soma_hairball,
dataset=flywire_dataset,
assert_id_match=assert_id_match)
# Confirm
viewer = navis.Viewer(title='Confirm skeletonization')
# Make sure viewer is actually visible and cleared
viewer.show()
viewer.clear()
# Add skeleton
viewer.add(n_fw, color='r')
msg = """
Please carefully inspect the skeletonization of the flywire mesh.
Hit ENTER to proceed if happy or CTRL-C to cancel.
"""
# Add mesh last - otherwise it might mask out other objects despite alpha
viewer.add(navis.MeshNeuron(mesh), color='w', alpha=.2)
try:
_ = input(msg)
except KeyboardInterrupt:
raise KeyboardInterrupt('Merge process aborted by user.')
except BaseException:
raise
finally:
viewer.close()
# Xform to FAFB
n_fafb = xform.flywire_to_fafb14(n_fw,
on_fail='raise',
coordinates='nm',
inplace=False)
mesh_fafb = xform.flywire_to_fafb14(tm.Trimesh(mesh.vertices, mesh.faces),
on_fail='raise',
coordinates='nm',
inplace=False)
# Heal neuron
n_fafb = navis.heal_fragmented_neuron(n_fafb)
# Merge neuron
return merge_into_catmaid(n_fafb,
target_instance=target_instance,
tag=tag,
mesh=mesh_fafb,
**kwargs)
def merge_flywire_neuron(id,
target_instance,
tag,
flywire_dataset='production',
assert_id_match=True,
drop_soma_hairball=True,
**kwargs):
"""Merge FlyWire neuron into FAFB CATMAID.
This function (1) fetches a mesh from FlyWire, (2) turns it into a skeleton,
(3) maps the coordinates to FAFB v14 space and (4) runs
``fafbseg.merge_neuron`` to merge the skeleton into CATMAID.
Disclaimer:
1. It is your responsibility to make sure that your export of FlyWire data
does not conflict with the FlyWire community guidelines. Mass export of
reconstructions is not OK!
2. As with all imports to CATMAID, the importing user is responsible for
the quality of the imported skeleton and to make sure no existing
tracings (including annotations) are negatively impacted.
Parameters
----------
id : int
ID of the FlyWire neuron you want to merge.
target_instance : pymaid.CatmaidInstance
Instance to merge the neuron into into.
tag : str
You personal tag to add as annotation once import into
CATMAID is complete.
dataset : str | CloudVolume
Against which FlyWire dataset to query::
- "production" (current production dataset, fly_v31)
- "sandbox" (i.e. fly_v26)
assert_id_match : bool
If True, will check if skeleton nodes map to the
correct segment ID and if not will move them back into
the segment. This is potentially very slow!
drop_soma_hairball : bool
If True, we will try to drop the hairball that is
typically created inside the soma.
**kwargs
Keyword arguments are passed on to ``fafbseg.merge_neuron``.
Examples
--------
Import a FlyWire neuron:
>>> _ = fafbseg.flywire.merge_flywire_neuron(id=720575940610453042,
... target_instance=manual,
... tag='WTCam')
"""
if not sk:
raise ImportError('Must install skeletor: pip3 install skeletor')
vol = parse_volume(flywire_dataset)
# Make sure this is a valid integer
id = int(id)
# Download the mesh
mesh = vol.mesh.get(id, deduplicate_chunk_boundaries=False)[id]
# Convert to neuron
n_fw = skeletonize_neuron(mesh,
remove_soma_hairball=drop_soma_hairball,
dataset=flywire_dataset,
assert_id_match=assert_id_match)
# Confirm
viewer = navis.Viewer(title='Confirm skeletonization')
# Make sure viewer is actually visible and cleared
viewer.show()
viewer.clear()
# Add skeleton
viewer.add(n_fw, color='r')
msg = """
Please carefully inspect the skeletonization of the FlyWire neuron.
Hit ENTER to proceed if happy or CTRL-C to cancel.
"""
# Add mesh last - otherwise it might mask out other objects despite alpha
viewer.add(navis.MeshNeuron(mesh), color='w', alpha=.2)
try:
_ = input(msg)
except KeyboardInterrupt:
raise KeyboardInterrupt('Merge process aborted by user.')
except BaseException:
raise
finally:
viewer.close()
# Xform to FAFB
n_fafb = xform.flywire_to_fafb14(n_fw,
on_fail='raise',
coordinates='nm',
inplace=False)
mesh_fafb = xform.flywire_to_fafb14(tm.Trimesh(mesh.vertices, mesh.faces),
on_fail='raise',
coordinates='nm',
inplace=False)
# Heal neuron
n_fafb = navis.heal_fragmented_neuron(n_fafb)
# Merge neuron
return merge_into_catmaid(n_fafb,
target_instance=target_instance,
tag=tag,
mesh=mesh_fafb,
**kwargs)