Annotations (cell types, etc.)
We currently store information about cells in a few different CAVE tables:
- cell_info: Cell type information.
- codex_annotations: More comprehensive cell type information that largely supersedes cell_info, though this is a work in progress with more details about how to use this table coming soon.
- backbone_proofread: Whether a neuron has received a first pass of proofreading to correct all major errors.
- neck_connective_y92500: Neurons that pass through the neck connective.
- peripheral_nerves: Neurons that pass through peripheral nerves (sensory and motor neurons).
Click here to see how to download tables using Python
You can download the contents of any one table in python as a pandas DataFrame via this sort of command:
import banc
from datetime import datetime, timezone
client = banc.get_caveclient()
df = client.materialize.live_live_query('put a table name here', datetime.now(timezone.utc))You can download the contents of all the tables via this command:
import banc
annotations_series = banc.lookup.all_annotations(group_by_segid=True)
annotations_df = banc.lookup.all_annotations(group_by_segid=False)This table contains information about cell types (e.g. sensory neuron vs motor neuron) and cell anatomy (e.g. descending vs ascending, soma on left vs soma on right). This is a hierarchically organized table – after a general annotation like sensory neuron is added, further annotations can be added to specify finer cell types, for instance chordotonal neuron, and then even finer with claw chordotonal neuron.
Proofreaders can query and upload to this table easily via the Slack app @banc-bot.
Here is the full list of annotations that can be posted to / found in this table:
-
sensory neuron
(axon enters the central nervous system via a peripheral nerve to bring in signals from the body – see also the section below "body part innervated")- photoreceptor neuron
- R7
- R8
- chordotonal neuron
- Johnston's organ neuron
- club chordotonal neuron
- claw chordotonal neuron
- hook chordotonal neuron
- bristle mechanosensory neuron
- bristle mechanosensory neuron at gustatory sensillum
- hair plate neuron
- campaniform sensillum neuron
- olfactory receptor neuron
- gustatory neuron
- thermosensory neuron
- hygrosensory neuron
- unknown sensory subtype
- photoreceptor neuron
-
CNS neuron
(any neuron that stays within the central nervous system, i.e. the brain and/or VNC)-
optic lobe intrinsic (click to expand)
- centrifugal
- C2
- C3
- distal medulla
- Dm1
- Dm2
- Dm3p
- Dm3q
- Dm3v
- Dm4
- Dm6
- Dm8a
- Dm8b
- Dm9
- Dm10
- Dm11
- Dm12
- Dm13
- Dm14
- Dm15
- Dm16
- Dm17
- Dm18
- Dm19
- Dm20
- distal medulla dorsal rim area
- DmDRA1
- DmDRA2
- lamina intrinsic
- Lai
- lamina monopolar
- L1
- L2
- L3
- L4
- L5
- lamina tangential
- Lat
- lamina wide field
- Lawf1
- Lawf2
- lobula intrinsic
- Li01
- Li02
- Li03
- Li04
- Li05
- Li06
- Li07
- Li08
- Li09
- Li10
- Li11
- Li12
- Li13
- Li14
- Li15
- Li16
- Li17
- Li18
- Li19
- Li20
- Li21
- Li22
- Li23
- Li24
- Li25
- Li26
- Li27
- Li28
- Li29
- Li30
- Li31
- Li32
- Li33
- lobula lobula plate tangential
- LLPt
- lobula medulla amacrine
- CT1
- LMa1
- LMa2
- LMa3
- LMa4
- LMa5
- lobula medulla tangential
- LMt1
- LMt2
- LMt3
- LMt4
- lobula plate intrinsic
- LPi01
- LPi02
- LPi03
- LPi04
- LPi05
- LPi06
- LPi07
- LPi08
- LPi09
- LPi10
- LPi11
- LPi12
- LPi13
- LPi14
- LPi15
- medulla intrinsic
- Mi1
- Mi2
- Mi4
- Mi9
- Mi10
- Mi13
- Mi14
- Mi15
- medulla lobula lobula plate amacrine
- Am1
- medulla lobula tangential
- MLt1
- MLt2
- MLt3
- MLt4
- MLt5
- MLt6
- MLt7
- MLt8
- proximal distal medulla tangential
- PDt
- proximal medulla
- Pm01
- Pm02
- Pm03
- Pm04
- Pm05
- Pm06
- Pm07
- Pm08
- Pm09
- Pm10
- Pm11
- Pm12
- Pm13
- Pm14
- serpentine medulla
- Sm01
- Sm02
- Sm03
- Sm04
- Sm05
- Sm06
- Sm07
- Sm08
- Sm09
- Sm10
- Sm11
- Sm12
- Sm13
- Sm14
- Sm15
- Sm16
- Sm17
- Sm18
- Sm19
- Sm20
- Sm21
- Sm22
- Sm23
- Sm24
- Sm25
- Sm26
- Sm27
- Sm28
- Sm29
- Sm30
- Sm31
- Sm32
- Sm33
- Sm34
- Sm35
- Sm36
- Sm37
- Sm38
- Sm39
- Sm40
- Sm41
- Sm42
- Sm43
- T1 neuron
- T1
- T2 neuron
- T2
- T2a
- T3 neuron
- T3
- T4 neuron
- T4a
- T4b
- T4c
- T4d
- T5 neuron
- T5a
- T5b
- T5c
- T5d
- translobula plate
- Tlp1
- Tlp4
- Tlp5
- Tlp14
- transmedullary
- Tm1
- Tm2
- Tm3
- Tm4
- Tm5a
- Tm5b
- Tm5c
- Tm5d
- Tm5e
- Tm5f
- Tm7
- Tm8a
- Tm8b
- Tm9
- Tm16
- Tm20
- Tm21
- Tm25
- Tm27
- Tm31
- Tm32
- Tm33
- Tm34
- Tm35
- Tm36
- Tm37
- transmedullary Y
- TmY3
- TmY4
- TmY5a
- TmY9q
- TmY9q__perp
- TmY10
- TmY11
- TmY14
- TmY15
- TmY16
- TmY20
- TmY31
- Y neuron
- Y1
- Y3
- Y4
- Y11
- Y12
- centrifugal
-
visual projection (click to expand)
- lobula columnar
- LC4
- LC6
- LC9
- LC10a
- LC10b
- LC10c
- LC10d
- LC10e
- LC10f
- LC11
- LC12
- LC13
- LC15
- LC16
- LC17
- LC18
- LC19
- LC20a
- LC20b
- LC21
- LC22
- LC24
- LC25
- LC26
- LC27
- LC28a
- LC29
- LC31a
- LC31b
- LC31c
- LC33a
- LC34
- LC35
- LC36
- LC37a
- LC39
- LC40
- LC41
- LC43
- LC44
- LC45
- LC46
- LCe01
- LCe01a
- LCe01b
- LCe02
- LCe03
- LCe04
- LCe05
- LCe06
- LCe07
- LCe08
- LCe09
- lobula tangential
- LT1a
- LT1b
- LT1c
- LT1d
- LT11
- LT43
- LT47
- LT51
- LT52
- LT53
- LT55
- LT57
- LT59
- LT60
- LT61a
- LT61b
- LT62
- LT63
- LT64
- LT65
- LT66
- LT67
- LT68
- LT69
- LT72
- LT73
- LT74
- LT75
- LT76
- LT77
- LT78
- LT79
- LT80
- LT81
- LT82a
- LT83
- LT84
- LT85
- LT86
- LT87
- LTe01
- LTe02
- LTe03
- LTe04
- LTe05
- LTe06
- LTe07
- LTe08
- LTe09
- LTe10
- LTe11
- LTe12
- LTe13
- LTe14
- LTe15
- LTe16
- LTe17
- LTe18
- LTe19
- LTe20
- LTe21
- LTe22
- LTe23
- LTe24
- LTe25
- LTe26
- LTe27
- LTe28
- LTe29
- LTe30
- LTe31
- LTe32
- LTe33
- LTe35
- LTe36
- LTe37
- LTe38a
- LTe38b
- LTe38c
- LTe40
- LTe41
- LTe42a
- LTe42b
- LTe42c
- LTe43
- LTe44
- LTe45
- LTe46
- LTe47
- LTe48
- LTe49a
- LTe49b
- LTe49c
- LTe49d
- LTe49e
- LTe49f
- LTe50
- LTe51
- LTe52a
- LTe52b
- LTe53
- LTe54
- LTe55
- LTe56
- LTe57
- LTe58
- LTe59
- LTe60
- LTe61
- LTe62
- LTe63
- LTe64
- LTe65
- LTe66
- LTe67
- LTe68
- LTe69
- LTe70
- LTe72
- LTe73
- LTe74
- LTe75
- LTe76
- lobula plate columnar
- LPC1
- LPC2
- lobula plate lobula columnar
- LPLC1
- LPLC2
- LPLC4
- lobula lobula plate columnar
- LLPC1
- LLPC2
- LLPC3
- LLPC4
- lobula plate tangential
- LPT04_HST
- LPT21
- LPT22
- LPT23
- LPT26
- LPT27
- LPT28
- LPT29
- LPT30
- LPT31
- LPT42_Nod4
- LPT47_vCal2
- LPT48_vCal3
- LPT49
- LPT50
- LPT51
- LPT52
- LPT54
- LPTe01
- LPTe02
- Nod1
- Nod2
- Nod3
- Nod5
- H2
- medulla medulla
- MeMe_e02
- MeMe_e03
- MeMe_e04
- MeMe_e05
- MeMe_e06
- MeMe_e07
- MeMe_e08
- medulla tubercle
- MeTu1
- MeTu2a
- MeTu2b
- MeTu3c
- MeTu3a
- MeTu3b
- MeTu4a
- MeTu4b
- MeTu4c
- MeTu4d
- MeTu4_unknown
- medulla lobula plate
- MeLp1
- amacrine medulla
- aMe1
- aMe3
- aMe5
- aMe6a
- aMe8
- aMe9
- aMe10
- aMe12
- aMe19a
- aMe19b
- aMe20
- aMe25
- aMe26
- vertical system
- VSm
- VS1
- VS2
- VS3
- VS4
- VS5
- VS6
- VS7
- VS8
- VST1
- VST2
- medulla tangential
- MTe01a
- MTe01b
- MTe02
- MTe03
- MTe04
- MTe05
- MTe06
- MTe07
- MTe08
- MTe09
- MTe10
- MTe11
- MTe12
- MTe13
- MTe14
- MTe15
- MTe16
- MTe17
- MTe18
- MTe19
- MTe20
- MTe21
- MTe22
- MTe23
- MTe24
- MTe25
- MTe26
- MTe27
- MTe28
- MTe29
- MTe30
- MTe31
- MTe32
- MTe33
- MTe34
- MTe35
- MTe36
- MTe37
- MTe38
- MTe39
- MTe40
- MTe41
- MTe42
- MTe43
- MTe44
- MTe45
- MTe46
- MTe47
- MTe48
- MTe49
- MTe50
- MTe51
- MTe52
- MTe53
- MTe54
- MC65
- horizontal system
- HSE
- HSN
- HSS
- lobula columnar
-
visual centrifugal (click to expand)
- lobula tangential
- LT34
- LT36
- LT37
- LT38
- LT39
- LT40
- LT41
- LT42
- LT56
- LT70
- lobula plate tangential
- LPT53
- LPT57
- LPT58
- amacrine medulla
- aMe4
- aMe17a1
- aMe17a2
- aMe17b
- aMe17c
- medial antennal lobula
- mALC3
- mALC4
- mALC5
- centrifugal medulla
- cM01a
- cM01b
- cM01c
- cM02a
- cM02b
- cM03
- cM04
- cM05
- cM06
- cM07
- cM08a
- cM08b
- cM08c
- cM09
- cM10
- cM11
- cM12
- cM13
- cM14
- cM15
- cM16
- cM17
- cM18
- cM19
- centrifugal medulla lobula
- cML01
- cML02
- centrifugal medulla lobula lobula plate
- cMLLP01
- cMLLP02
- centrifugal lobula
- cL01
- cL02a
- cL02b
- cL02c
- cL02d
- cL03
- cL04
- cL05
- cL06
- cL07
- cL08
- cL09
- cL10
- cL11
- cL12
- cL13
- cL14
- cL15
- cL16
- cL17
- cL18
- cL19
- cL20
- cL21
- cL22a
- cL22b
- cL22c
- centrifugal lobula medulla
- cLM01
- centrifugal lobula plate
- cLP01
- cLP02
- cLP03
- cLP04
- cLP05
- cLPL01
- centrifugal lobula lobula plate
- cLLP02
- centrifugal lobula lobula plate medulla
- cLLPM01
- cLLPM02
- ventral centrifugal
- VCH
- optic anterior
- OA-AL2b1
- OA-AL2b2
- OA-AL2i1
- OA-AL2i2
- OA-AL2i3
- OA-AL2i4
- OA-ASM1
- lobula tangential
- central brain intrinsic
- VNC intrinsic
-
-
efferent neuron
(has a cell body in the central nervous system & axon leaves through a peripheral nerve to innervate something in the body – see also the section below "body part innervated")- motor neuron
(a neuron that releases glutamate directly onto muscle fibers to cause them to them contract) - UM neuron
(unpaired median neuron: an efferent neuron with a midline soma and symmetric bilateral projections) - endocrine neuron
(a neuron that secretes hormones or innervates a hormone-producing gland)
- motor neuron
-
glia
(for examples of glial subtypes, see image below from Kremer et al. 2017 Glia)- trachea
- astrocyte
- cortex glia
- neuropil ensheathing glia (shown in the figure below as just "ensheathing glia")
- nervous system ensheathing glia
- perineural glia
- subperineural glia
0A, 0B, 1A, 1B, 2A, 3A, 3B, 4A, 4B, 5B, 6A, 6B, 7B, 8A, 8B, 9A, 9B, 10B, 11A, 11B, 12A, 12B, 13A, 13B, 14A, 14B, 15B, 16B, 17A, 18B, 19A, 19B, 20A/22A, 21A, 23B, 24A, 24B
- cholinergic
- GABAergic
- glutamatergic
- dopaminergic
- histaminergic
- octopaminergic
- serotonergic
- tyraminergic
- soma on left
- soma on midline
- soma on right
- soma in brain
- soma in central brain
- soma in optic lobe
- soma in neck connective
- soma in VNC
- soma in T1
- soma in T2
- soma in T3
- soma in abdominal ganglion
- descending
(axon comes from the brain to the VNC via the neck connective) - ascending
(axon goes from the VNC to the brain via the neck connective)
- leg local
(innervates only 1 leg neuromere, or the 2 neuromeres for a left-right pair of legs. This annotation does NOT indicate that the cell innervates ONLY the leg neuromeres – the cell can also innervate other non-leg-neuromere regions like tectulum.)- T1 leg local
- T2 leg local
- T3 leg local
- leg intersegmental
(innervates neuromeres for multiple pairs of legs. This annotation does NOT indicate that the cell innervates ONLY the leg neuromeres – the cell can also innervate other non-leg-neuromere regions like tectulum.)- T1+T2 leg intersegmental
- T1-to-T2 leg intersegmental
- T2-to-T1 leg intersegmental
- T1+T3 leg intersegmental
- T1-to-T3 leg intersegmental
- T3-to-T1 leg intersegmental
- T2+T3 leg intersegmental
- T2-to-T3 leg intersegmental
- T3-to-T2 leg intersegmental
- T1+T2+T3 leg intersegmental
- T1+T2 leg intersegmental
- teculum local
(innervates only 1 segment of the teculum. This annotation does NOT indicate that the cell innervates ONLY the tectulum – the cell can also innervate other non-tectulum regions like the leg neuromeres.)- neck tectulum local
- wing tectulum local
- haltere tectulum local
- tectulum intersegmental
(innervates multiple segments of the tectulum. This annotation does NOT indicate that the cell innervates ONLY the tectulum – the cell can also innervate other non-tectulum regions like the leg neuromeres.)- neck+wing tectulum intersegmental
- neck-to-wing tectulum intersegmental
- wing-to-neck tectulum intersegmental
- neck+haltere tectulum intersegmental
- neck-to-haltere tectulum intersegmental
- haltere-to-neck tectulum intersegmental
- wing+haltere tectulum intersegmental
- wing-to-neck tectulum intersegmental
- haltere-to-wing tectulum intersegmental
- neck+wing+haltere teculum intersegmental
- neck+wing tectulum intersegmental
- unilateral
(all synaptic connections are on one side of the midplane) - bilateral
(makes synaptic connections on both sides of the midplane) - midplane
(all or nearly all branches stay near the midplane)
Note that these annotations can apply to both sensory neurons and motor neurons
- innervates antenna
- innervates scape
- innervates pedicel
- innervates funiculus
- innervates sacculus
- innervates arista
- innervates maxillary palp
- innervates proboscis
- innervates retina
- innervates ocelli
- innervates neck
- innervates corpus cardiacum
- innervates corpus allatum
- innervates aorta
- innervates leg
- innervates T1 leg
- innervates thorax
- innervates thorax-coxa joint
- innervates coxa
- innervates coxa-trochanter joint
- innervates trochanter
- innervates femur
- innervates femur-tibia joint
- innervates tibia
- innervates tibia-tarsus joint
- innervates tarsus
- innervates T2 leg
- innervates thorax
- innervates thorax-coxa joint
- innervates coxa
- innervates coxa-trochanter joint
- innervates trochanter
- innervates femur
- innervates femur-tibia joint
- innervates tibia
- innervates tibia-tarsus joint
- innervates tarsus
- innervates T3 leg
- innervates thorax
- innervates thorax-coxa joint
- innervates coxa
- innervates coxa-trochanter joint
- innervates trochanter
- innervates femur
- innervates femur-tibia joint
- innervates tibia
- innervates tibia-tarsus joint
- innervates tarsus
- innervates T1 leg
- innervates notum
- innervates scutum
- innervates scutellum
- innervates wing
- innervates haltere
- innervates spiracle
- innervates abdomen
- innervates left side of body
- innervates right side of body
- innervates both sides of body
These muscle names come from Azevedo, Lesser, Phelps, Mark et al. 2024 Nature
- innervates tergopleural promotor
- innervates pleural promotor
- innervates pleural remotor and abductor
- innervates sternal anterior rotator
- innervates sternal posterior rotator
- innervates sternal adductor
- innervates tergotrochanter extensor
- innervates sternotrochanter extensor
- innervates trochanter extensor
- innervates trochanter flexor
- innervates accessory trochanter flexor
- innervates femur reductor
- innervates tibia extensor
- innervates tibia flexor
- innervates accessory tibia flexor
- innervates tarsus depressor
- innervates tarsus retro depressor
- innervates tarsus levator
- innervates long tendon muscle
- innervates long tendon muscle 2
- innervates long tendon muscle 1
- innervates indirect flight muscle
- innervates dorsal longitudinal muscle
- innervates dorsoventral muscle
- innervates wing steering muscle
- innervates wing tension muscle
Freeform text annotations indicating a neuron's specific cell type / name / identity
Freeform text annotations not related to a neuron's specific cell type / name / identity
This table lists cells that have received a first pass of proofreading (usually between 5 and 60 minutes of work), meaning the overall morphology of the cell is expected to be correct. Many small branches may still be missing at this point, but future proofreading is not expected to radically alter the shape or connectivity of the neuron.
This table contains additional text tags that have been placed on neurons in the process of proofreading. The table accepts a fixed list of terms:
- roughly proofread
(a step down from "backbone_proofread" – this means that the neuron is in good enough shape to have its general cell type identified, but it may not yet have its whole backbone present) - thoroughly proofread
(a step up from "backbone_proofread" – this means nearly that you can assume that any future edits won't do anything more than add or subtract a small number of synapses / a few short thin branches) - soma is damaged
(damage to the nervous system has made it impossible to connect this segment with its soma) - arbor is damaged
(damage to the nervous system has made it impossible to complete the main arbor of this segment) - large fragment
(a significant fraction of a neuron that is clearly missing some other sigificant fraction of its arbor, which can't easily be proofread further, often due to dataset damage) - merge monster
(giant difficult-to-proofread objects that existed in the initial AI-generated segmentation and have not yet been split apart into realistic cells)