Supplemental_files_columns.md

Explanation of columns for Supplemental_file1_neuron_annotations.tsv and Supplemental_file2_non_neuron_annotations.tsv

• pos_x, pos_y, pos_z are anchor coordinates in 4x4x40nm voxel space (typically on the backbone of the neuron) for given neuron
• supervoxel_id is the ID of the supervoxel the anchor coordinates map to
• root_id is the ID of the neuron in the FlyWire 783 release
• soma_x, soma_y, soma_z are soma coordinates in 4x4x40nm voxel space
• nucleus_id maps to the nucleus detection table (available through CAVE); neurons with soma_x/y/z but without nucleus_id have had their soma manually marked
• flow, super_class, cell_class, cell_sub_class, cell_type, hemibrain_type are the hierarchical annotations
• ito_lee_hemilineage and hartenstein_hemilineage provide the hemilineage in ItoLee and Hartenstein nomenclature; note that not all labels exist in the Hartenstein nomenclature
• morphology_group provides a coarse morphological grouping based on hemilineage clustering
• top_nt is the top predicted neurotransmitter for the given neuron, calculated by averaging confidences over the transmitter predictions for all presynapses for the given neuron and choosing the most confident transmitter
• top_nt_conf is the average confidence for the top neurotransmitter
• side refers to the soma side for brain-intrinsic neurons and the nerve-entry side for sensory/ascending neurons
• fbbt_id and vfb_id provide mappings to the database of the VirtualFlyBrain; the former is used for ontology terms (like cell types), the latter is an identifier for individual neurons
• status records a number of outliers: outlier_seg are neurons with segmentation issues (often due to dark cytosol); outlier_bio are neurons with small to medium sized differences (e.g. extra branches) compared with their contralateral or hemibrain homologues

Explanation of columns for Supplemental_file3_summary_with_ngl_links.csv

• ito_lee_hemilineage and hartenstein_hemilineage provide the hemilineage in ItoLee and Hartenstein nomenclature; note that not all labels exist in the Hartenstein nomenclature.
• notes records some of our observations of select published clones.
• ito_lee_lineage and hartenstein_lineage provide the corresponding lineage names to the hemilineages.
• hemibrain_map contains the rough* mapping of that hemilineage to a hemibrain cell body fiber.
• is_hemilineage contains our best guesses on whether the entry is a hemilineage or not:
  • H(NT): we guess that this is a hemilineage (instead of a combination of two hemilineages of one lineage) based on the neurotransmitter information from Eckstein et al. (2024);
  • 2L_1NT: 2 lineages, all neurons are predicted the same neurotransmitter;
  • H: a hemilineage;
  • H/L: a hemilineage or lineage;
  • H?: we think it is a hemilineage, but we are not certain;
  • H_2NT: we think it is a hemilineage, but the neurons are predicted to have 2 neurotransmitters;
  • Hp: probably a hemilineage;
  • L: lineage;
  • T2: neurons in this cell body fibre tract belong to a type II lineage.
• *ngl_link ( , left_, right_ and hemibrain_) columns contain neuroglancer links with the neurons in that hemilineage selected, on that side, and coloured based on the morphological groups. Each morphological group is in a separate layer (in addition, FlyWire and hemibrain neurons are in separate layers). There is also a de-selected layer that contains all neurons in that hemilineage in FlyWire.
• ids_* (left, right, center, hb) colunms contain the neuron ids for that hemilineage in that side.
• id_count_* (left, right, center, hb) columns contain the neuron count for that hemilineage in that side.
• n_clusters_* (left, right, hb) columns contain the number of clusters for that hemilineage in that side.
• shape_truncated and number_truncated columns contain information on whether the hemilineage is truncated in shape/number in the hemibrain.

Explanation of columns for Supplemental_file4_hemilineages_clustering.csv

• root_id is the ID of the neuron in the FlyWire 783 release.
• persistent_cluster column contains the side_cluster labels of neurons that cluster together across one-, two- and three-hemisphere clustering (see the Morphological groups section in Methods).
• side is the hemisphere (left/right/hemibrain) the neuron is in.
• ito_lee_hemilineage and hartenstein_hemilineage provide the hemilineage in ItoLee and Hartenstein nomenclature; note that not all labels exist in the Hartenstein nomenclature.
• hemilineage_group records the morphological groups.
• supervoxel_id corresponds to the supervoxel_ids in the Supplemental_file1_neuron_annotations.tsv file. The value is NA if the neuron is from the hemibrain.
• nps column contains the top-three innervated neuropils, alphabetically sorted, for that neuron.
• The data can be read using the following code in Python:

  import pandas as pd 
  supp4 = pd.read_csv(
    'https://raw.githubusercontent.com/flyconnectome/flywire_annotations/main/supplemental_files/Supplemental_file4_hemilineages_clustering.csv', 
    index_col=0, dtype = {'supervoxel_id': 'Int64'})
  

Explanation of columms for Supplemental_file5_hemibrain_meta.csv

The following columns correspond 1:1 to columns shown/available for download through neuPrint: bodyId, type, notes, status, cellBodyFiber, somaLocation, pre, post and cropped.

We additionally added the following columns:

• in morphology_type we collapsed connectivity types back into morphology types (i.e. removed the _a, _b, etc. suffixes)
• cell_class contains labels analogous to those the cell class labels we provide for FlyWire neurons
• side refers to the soma side and is principally based on the instance column where an _L and _R typically indicates the side; we did however make a sizeable number of manual adjustments
• pre_con2 contains the number of outgoing connections for a given neuron whereas pre contains the number of presynapses (remember that insect synapses are polyadic); these numbers were used to compare hemibrain vs FlyWire presynapse counts
• fbbt_id contains a FBbt ID that maps to the entry for a given hemibrain type in the VirtualFlyBrain database
• ito_lee_hemilineage provide identified hemilineages in ItoLee nomenclature
• morphology_group provides a coarse morphological grouping based on hemilineage clustering