Supplemental Files for Eckstein and Bates et al., Cell (2024)

synister_fw_mat571_t11_synapses.feather - synapse level transmitter predictions for the FAFB dataset
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Columns:id          :   pre-synapse ID
pre         :   neuron ID of pre-synaptic neuron
post        :   neuron ID of post-synaptic neuron
pre_pt_position_{x, y,  z}  : coordinates of pre-synapse in nm
nts_11.*    :   predicted score for being one of the six neurotransmitter types (or "neither")

hemibrain-v1.2-tbar-neurotransmitters.feather.bz2 - synapse level transmitter predictions for the hemibrain dataset
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Columns:x, y, z     :   voxel coordinates of pre-synapse
conf        :   confidence value of synapse detection
sv          :   supervoxel ID of the pre-synapse
roi         :   name of brain region of pre-synapse
roi_label   :   numerical label of brain region of pre-synapse
body        :   body ID of the pre-synaptic neuron
nts_8.*     :   predicted score for being one of the six neurotransmitter types (or "neither")

Neuprint_Synapses_manc_v1.ftr - synapse level transmitter predictions for the MANC dataset
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From Takemura et al. 2023, made with the network and methods described in this repository:  https://www.biorxiv.org/content/10.1101/2023.06.05.543757v1

Columns:x, y, z     :   voxel coordinates of pre-synapse
conf        :   confidence value of synapse detection
sv          :   supervoxel ID of the pre-synapse
roi         :   name of brain region of pre-synapse
roi_label   :   numerical label of brain region of pre-synapse
body        :   body ID of the pre-synaptic neuron

synister-master.zip - code for training and prediction with the 'synister' pipeline for neurotransmission
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A clone of out GitHub repository at the time of paper release, found at: https://github.com/funkelab/synister, e738e22.

Contains README with in-depth description.

supplemental_data_1.csv - original ground truth data by identified cell type
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A .csv file that provides each

cell_type     :   cell type we used to generate our ground truth data,

known_nt     :   the transmitter it is has been reported to express from the literature

known_source     :   the study that made this report and

evidence     :   the type of evidence it contained

Note that we used this data to build our original ground truth, but have since made a wider effort to annotate known transmission for validation, reflected in Supplemental data 3 and 4, columns known_nt and known_source.

supplemental_data_2.csv - original ground truth data by individual connectomic neuronal reconstruction
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A .csv file that indicates each neuronal reconstruction used to generate our ground-truth data. Presynapses from each reconstruction were used.

id     :   a unique identifier, which is the root ID for a flywire neuron, a skeleton ID for a FAFB-Catmaid neuron and a bodyid for a HemiBrain neuron,

known_nt     :   the designated transmitter from the literature

cell_type     :   its cell type and

dataset     :   the dataset from which the neuron comes.

FAFB-Catmaid reconstructions can be found on virtual fly brain: https://fafb.catmaid.virtualflybrain.org/. Flywire reconstructions can be found at: https://ngl.flywire.ai/. HemiBrain reconstructions can be found at: https://neuprint.janelia.org/?dataset=hemibrain. We used version 630 in this study.

supplemental_data_3.csv - 
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A .csv file in which each row is a single identified HemiBrain reconstruction. Columns provide:

bodyid     :   each neuron’s unique identifier 

cell_type     :   morphological cell type

pre     :   number of output synapses

cropped     :   whether or not the neuronal reconstruction is cut off by the HemiBrain volume

conf_nt     :   neuron-level transmitter prediction

conf_nt_p     :   the confidence score for that prediction, which was calculated using the synapse-level confusion metrics and with synapse filtering

top_nt, top_nt_p     :   neuron-level transmitter prediction with no synapse filtering for axon/dendrite

{transmitter name}     :   the proportion of synapse-level transmitter predictions that “voted” for each transmitter 

segregation_index     :   the segregation index, a measure of neuronal polarity

projection_score     :   the projection score, a measure of the distance between axon and dendrite

ito_lee_hemilineage, hartenstein_hemilineage     :   the hemilineage to which this neuron belongs

in_ground_truth     :   whether or not presynapses from this neuron were included in our ground-truth data

supplemental_data_4.csv - 
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A .csv file where each row is a single identified FAFB-FlyWire reconstruction. Columns provide:

root_id_630     :   each neuron’s unique identifier from the 630 materialization of the FAFB-FlyWire dataset used in this paper

root_id_783     :   each neuron’s unique identifier from the new 783 materialization of the FAFB-FlyWire dataset used in this paper

cell_type     :   morphological cell type

conf_nt     :   neuron-level transmitter prediction

conf_nt_p     :   the confidence score for that prediction, which was calculated using the synapse-level confusion metrics and with synapse filtering

top_nt, top_nt_p     :   neuron-level transmitter prediction with no synapse filtering for axon/dendrite

{transmitter name}     :   the proportion of synapse-level transmitter predictions that “voted” for each transmitter 

segregation_index     :   the segregation index, a measure of neuronal polarity

projection_score     :   the projection score, a measure of the distance between axon and dendrite

ito_lee_hemilineage, hartenstein_hemilineage     :   the hemilineage to which this neuron belongs

side, morphology group, flow, cell class, cell sub class      :   other metadata from Schlegel et al. 2023, https://zenodo.org/records/8077335

in_ground_truth     :   whether or not presynapses from this neuron were included in our ground-truth data

notes     :   extra notes on the cell type designation, including alternate names

pos_x, pos_y, pos_z     :   because the root id for neurons is changing as neurons are edited in an active connectome project we also supply the position of a point in the neuron to help identify it in FAFB-FlyWire voxel space

nucleus_id     :   an ID for the nucleus segmentation

supplemental_data_5.zip - 
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A .zip archive containing .png files depicting each of the 183 brain hemilineages we have used from the FAFB-FlyWire dataset. Neurons in each hemilineage are colored by their neuron-level transmitter predictions, hemilineage names given in the file name. Hemilineage labels for the FAFB-FlyWire dataset are fully reported in Schlegel et al. 2023, https://zenodo.org/records/8077335.

supplemental_data_6.csv - 
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A .csv containing summary results for our 183 central brain secondary hemilineages. Columns provide:

ito_lee_hemilineage     :   each hemilineage’s name 

hartenstein_hemilineage     :   and lineage-associated tract

left, right, center     :   the number of neurons on the left and right hemispheres (left, right, center),

lineage_type     :   the lineage type i.e. Type I or II

{transmitter}     :   the number of neurons predicted for each transmitter

majority_nt     :   and the majority vote of the hemilineage.

Note, the same information is given for HemiBrain hemilineages, with ‘hemibrain ’ added to the column name.

supplemental_data_7.csv - 
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A .csv in which each row is a described cell type of the fly brain. Cell type annotations were drawn from Schlegel et al. 2023, neurons with no cell type or hemibrain type annotated are not included. Columns provide:

cell_type     :   each cell type’s name

cell_type_nt     :   predicted transmitter for the cell type (cell type nt)

cell_type_confidence     :   the cell type level transmitter confidence score

{transmitter}_{dataset}_confidence     :   the sum of neuronlevel transmitter predictions across all FAFB-FlyWire reconstructions for each transmitter

{transmitter}_{dataset }_n     :   the number of neurons with that confidence,

known_nt     :   the transmitters reported to be used by the cell type in the literature

known_nt_source     :   the citations for that information 

ito_lee_hemilineage, hartenstein_hemilineage, morphology_group, flow, cell_class, cell_sub_class     :   morphological annotations from Schlegel et al. 2023

cell_type_nt     :   the cell type level transmitter is determined by the highest {transmitter} cell type {dataset} confidence

cell_type_nt_conf     :   The cell type level transmitter confidence score (cell type nt) was calculated using our prediction confusion matrices.

Results for both FAFB-FlyWire (‘ fafb’) and HemiBrain (‘hemibrain’) datasets are given.

supplemental_data_8.tar.gz
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Contains PNG files of 2D images cropped around synapses, together with their
counterfactual translations into different neurotransmitter types and
highlights of the most important areas for classification.There is one PNG file for each pair of neurotransmitters, named
`{source}_{target}.png`. E.g., the file `ach_dop.png` contains translations of
real cholinergic synapses into counterfactual dopaminergic synapses.Each PNG shows images in six columns, which are:1: original raw + classifier scores
2: counterfactual raw + classifier scores
3: counterfactual raw, with original raw in mask + classifier scores
4: mask, shown on original + relative classifier change
5: mask, shown on counterfactual
6: difference in mask area

Paper: https://www.cell.com/cell/fulltext/S0092-8674(24)00307-6