A chronological record of additions, changes and fixes made to Coda. Where a change can be tried, Open example loads a working workflow in the editor. The examples run on synthetic data in your browser, so they open without an account.
Dynamically extend functionality, save sets of nodes you use often, and get informed when new features land.
Chronologically list of all changes to Coda. Where a change can be tried, Open example loads a working workflow in the editor.
When a new feature drops, Coda shows a short note the next time you open it. You can find the note again under ? ▸ What’s New.
Nodes are now organised into plugins. The initial set includes Connectome, ZapBench and Cortex. Switch off the ones you don’t use under ⋯ ▸ Plugins. Workflows that already use them still open and run.
In the future, selecting sets of plugins will allow you to fully customise Coda to your specific needs.
The first new plugin is Cortex, with the Cortex Gallery for browsing MICrONS cells by type and cortical depth. Go to coda.science/cortex to open Coda with it switched on.
Also in this update
Select a set of nodes, right-click ▸ Save as Recipe…. The recipe can then be added to any workflow via the + button, the command palette or the context menu.
A FlyWire FAFB node on its own uses cell-type labels that have since been updated. The node now says so and offers a one-click fix that adds the current annotation tables.
The CAVE table node’s settings are simpler, and CAVE neuron thumbnails load more reliably.
Speeds up all connectivity queries.
Custom CAVE now lets you change the default synapse table and other settings.
Sources that publish region IDs but no names can now be drawn.
Sankey, Flow Chart and Rank Plot show how signals move through a circuit, and new nodes find, place and count synapses.
Connect an Influence node’s Transfers output and see how drive spreads from your seed neurons through each layer. The caption tells you how far the diagram is from conserving flow, because synapse counts usually don’t.
Boxes sized to their labels, arrows routed around them, and a synapse count on every arrow. Built for the tens of neurons a Paths search returns, where the Network Viewer is built for thousands. Feedback connections are drawn dashed so they are not mistaken for feed-forward ones.
Scores on a log axis by rank, with the running share of the total underneath, so you can see how many neurons account for most of an influence score. Seed neurons are ringed and left out of the share.
Set Cell shape to circles and each cell’s size shows its value as well as its colour. On a sparse matrix the pattern stands out, because empty cells stay blank.
Also in this update
NeuronBridge.Find the light-microscopy lines that match an EM neuron, using Janelia’s NeuronBridge index. You can also choose it as an analysis in the Workflow Wizard.
Select Neurons.Pick neurons out of a set by rules on their attributes. Open example →
Synapses Between and Synapses to Edges.Get the synapses between two sets of neurons, then count them into an edge list, optionally split by region. Open example →
Points in Volumes.Label each synapse with the brain region, or any mesh, it sits inside. Open example →
Distance between (preview).The closest approach, mean or median distance between skeletons and meshes. Open example →
Upload Mesh.Bring your own OBJ, PLY or STL into the 3D View.
A sign-in window replaces copying a token from the neuPrint website.
Meshes also has an explicit Downsample setting. Full resolution is the default.
Connection weights can be divided by each neuron’s total input or output, and Paths reports how many neurons each step covers.
The Coda MCP server lets Claude and other assistants build workflows for you and hand back a link that opens them.
The node browser describes each node as you hover it, and warning messages across nodes are clearer.
ZapBench calcium recordings can now be joined to connectome neurons, and the editor shows more about what is on each wire.
Cell IDs, ZapBench Traces, ZapBench to Neurons and Neurons to ZapBench Traces.Read whole-brain calcium activity from the larval zebrafish, and go from its cells to connectome neurons and back.
Embedding.UMAP of a feature or similarity matrix, reproducible with a fixed seed. Open example →
Reduce Matrix and Attach Attributes.Collapse a matrix to one value per row or column (mean, sum, spread), and add columns from a table to skeletons or meshes. Open example →
After a run, hovering a node’s output socket shows what it holds: columns, a row, the size.
Attach a short note to any node for whoever opens the workflow next.
A new guide under ? ▸ Guides labels every control on screen at once.
Click a mesh to select it; unselected neurons fade. Skeletons are drawn at their real thickness.
Select rows and columns by dragging, and rename axis labels, for example from IDs to cell types.
Animated thumbnails on hover, small distribution plots, and a guide for the expanded view.
Custom CAVE can point at any CAVE server, not only the public ones.
Open the graph in Cytoscape Web with one click.
The status bar shows how much memory Coda is using, and the top-left menu can Clone and Rename workflows.
The toolbar folds into a menu instead of zooming the whole page out.
The Workflow Wizard can build one workflow over several datasets at once, and every node guide entry opens a working example.
Choose two or more connectomes in the Wizard’s first question and it builds one workflow that stacks them, offering only the analyses every chosen dataset supports. Generated workflows are laid out automatically and carry a note explaining each step.
Also in this update
Split Neurons.Divide skeletons or meshes into two groups by a rule, with Carry fields to bring any column along. Open example →
Zoom and pan, and rename leaves from an annotation table. Open example →
Including cell type, so a profile can describe a whole type rather than one neuron.
Every entry has Open in a workflow and a See also list.
The Dashboard shows a progress bar while it runs, and ⌘A selects every node.
A lean mode and a reasoning mode, and a Send run values switch for keeping results out of the conversation.
It used to return the whole dataset, which could start a very large query as soon as the node was dropped on the canvas. Add a filter or a region to get neurons back. Saved workflows that relied on the old behaviour will show an empty table.
Every data source now publishes neuronId as text rather than a number. Long CAVE IDs no longer lose digits, and neuPrint and CAVE tables can be stacked together. If you export a table and join it elsewhere, the ID column type has changed.
Coda opens to everyone as a public beta: a node-graph editor for connectome analysis that runs in your browser.
Wire nodes together to query a connectome, reshape the answer and draw it: partners, paths, influence, morphology and more, over neuPrint, CAVE and CATMAID datasets. Nothing to install; it runs in your browser.
New to it? The Workflow Wizard builds a first workflow from four questions, the field guide explains the ideas, and the node guide describes every node.