FlyWire Codex Workshop

28 Oct 2025

>53,000 Codex Users

1,502,911 searches

Mar 22, 2023 to Sep 21, 2025

Top 10,000: >18

Top 1,000: >469

Top 100: >6,613

How many queries does it take to make it to the Codex 100?

Queries & Resources

• Examples of advances queries:
1. https://codex.flywire.ai/sample_queries�
• How to use the downstream_union operator.
• https://codex.flywire.ai/app/search?dataset=fafb&filter_string=%7Bdownstream_union%7D+class+%3D%3D+ocellar&sort_by=&page_size=10
• How to find neurons belonging to a set of classes and upstream/downstream of others.
• e.g.: https://codex.flywire.ai/app/search?dataset=fafb&filter_string=%7Bdownstream%7D+720575940644751652+%26%26+class+%3D%3D+AN&sort_by=&page_size=10�
• Queries for receptor types/NT expression (e.g., GABAergic circuits).
• e.g.: https://codex.flywire.ai/app/search?dataset=fafb&filter_string=nt_type+%3D%3D+GABA&sort_by=&page_size=10�
• How to run queries for cell_types with processes in a region (e.g., protocerebral bridge) and their connectivity.
• https://codex.flywire.ai/app/neuropils?dataset=fafb&selected=PB
• How to look for neurons with soma in a certain neuropil.�
• How to identify split Gal4 lines for neurons explored in Codex.
• Follow links to: VFB, FlyBase, Braincircuits.io, NeuronBridge, e.g.: https://codex.flywire.ai/app/search?dataset=fafb&filter_string=dm4&sort_by=&page_size=10�
• Reverse search: from driver lines (GAL4, LexA, split-GAL4) to neurons.
• Not available yet�

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Connectivity & Pathways

• Shortest and strongest paths, “influence” metrics.
1. https://codex.flywire.ai/app/downstream_influence?q=id+%3D%3D+720575941353100336&dataset=banc
• How to interpret/find reference for “Effector Influence (top out)” in BANC.
• Details in manuscript and github repo: https://www.biorxiv.org/content/10.1101/2025.07.31.667571v2�
• How to download and merge connectivity maps.
• https://codex.flywire.ai/app/connectivity?dataset=banc&cell_names_or_ids=__sample_cells__
• Click download CSV or JSON�
• Synapse counts, neurotransmitter detection, and synapse spatial distributions.
• https://codex.flywire.ai/api/download?dataset=fafb
• Download raw data

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• Normalised pathway analyses (% of recipient’s total input).
• Coming soon�

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Visualization & Interface

• Show neuropil names.
1. https://codex.flywire.ai/app/neuropils?dataset=fafb&selected=AME_R,LA_R,LO_R,LOP_R,ME_R��
• Toggle synapse visibility on/off.
• https://codex.flywire.ai/app/view_3d?query=root_id+%3D%3D+720575940632852124&dataset=fafb��
• More toggles/info in network widget.
• https://codex.flywire.ai/app/connectivity?dataset=fafb&cell_names_or_ids=__sample_cells__&download=��
• Color by hemilineage.
• https://codex.flywire.ai/app/view_3d?dataset=fafb&query=hemilineage+%7Bstarts_with%7D+LB&action=random_sample&color_by=Hemilineage&mode=No+EM�
• Better figure-building / creating images + More visualization and analysis tools for connectome.
• Coming soon

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Advanced Analysis

• Motif analysis: finding instances of motifs from Murthy’s 2024 network statistics paper.
1. e.g. https://codex.flywire.ai/app/motifs/?dataset=fafb&enabledAB=on&regionAB=Any&minSynapseCountAB=1&ntTypeAB=Any&enabledBA=on&regionBA=Any&minSynapseCountBA=1&ntTypeBA=Any&enabledAC=on&regionAC=Any&minSynapseCountAC=1&ntTypeAC=Any&enabledCA=on&regionCA=Any&minSynapseCountCA=1&ntTypeCA=Any&enabledBC=on&regionBC=Any&minSynapseCountBC=1&ntTypeBC=Any&enabledCB=on&regionCB=Any&minSynapseCountCB=1&ntTypeCB=Any&queryA=&queryB=&queryC=��
• Gut–brain axis analysis using receptor expression and connectivity (Angel Torres-Roman).
• https://codex.flywire.ai/app/path_length?dataset=banc&source_cell_names_or_ids=720575941645177720&target_cell_names_or_ids=720575941451015802&min_syn_count=3&group_by=��
• Tools for tracing neuron paths and narrowing presynaptic/postsynaptic partners.
• https://codex.flywire.ai/app/view_3d?dataset=fafb&query=720575940615850646&action=&color_by=&palette=Default&mode=No+EM��
• Attribute reference: request for a “cheatsheet” explaining neuron attributes.
• https://codex.flywire.ai/faq
• https://codex.flywire.ai/sample_queries?dataset=fafb��

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Datasets & Integration

• Bridging Codex datasets (FlyWire, BANC, MANC, MCNS).
1. https://codex.flywire.ai/app/cell_type_counts?dataset=fafb
2. Also see cross-dataset links in search results�
• Open-source availability?
• https://github.com/murthylab/codex�
• Access all connectomes in one place, even raw EM + Integrate NT/receptor data with morphology and connectivity. Can it be used for H01 and Fish1 datasets?
• That’s our mission�

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