We’ve expanded the Codex feature suite to include new attributes, search operators and analysis tools. On Oct 28, 2025, FlyWire held a Codex Workshop to highlight new features. Thanks to the 60+ people who attended on Zoom.

A recording of the event can be found on FlyWire YouTube:

Content in the workshop centered about submitted questions. The slide deck is available here and includes numerous example Codex queries, which are also listed below. Please continue to share your feedback/questions/ideas via the feedback icon on the top right of codex.flywire.ai.

Queries & Resources

• Examples of advanced queries:
  1. https://codex.flywire.ai/sample_queries
     
• How to use the downstream_union operator.
  1. 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.
  1. 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).
  1. 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.
  1. https://codex.flywire.ai/app/neuropils?dataset=fafb&selected=PB
  2. How to look for neurons with soma in a certain neuropil.
     
• How to identify split Gal4 lines for neurons explored in Codex.
  1. 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.
  1. Not available yet
     

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.
  1. Details in manuscript and github repo: https://www.biorxiv.org/content/10.1101/2025.07.31.667571v2
     
• How to download and merge connectivity maps.
  1. https://codex.flywire.ai/app/connectivity?dataset=banc&cell_names_or_ids=__sample_cells__
  2. Click download CSV or JSON
     
• Synapse counts, neurotransmitter detection, and synapse spatial distributions.
  1. https://codex.flywire.ai/api/download?dataset=fafb
  2. Download raw data 

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

Coming soon

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.
  1. https://codex.flywire.ai/app/view_3d?query=root_id+%3D%3D+720575940632852124&dataset=fafb
     
     
• More toggles/info in network widget.
  1. https://codex.flywire.ai/app/connectivity?dataset=fafb&cell_names_or_ids=__sample_cells__&download=
     
     
• Color by hemilineage.
  1. 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.
  1. Coming soon

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).
  1. 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.
  1. 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.
  1. https://codex.flywire.ai/faq

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?
  1. 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