Orr Biologicals / Open biological intelligence

Open tools for
biological discovery.

We develop computational biology platforms, scientific software and research instrumentation for understanding complex living systems.

Explore NeuroML Read our approach

Current focus: Mouse & fly connectomics
Also building: Algae · single cells
Standard: Evidence over assertion

Two-dimensional projection of the measured skeleton of MICrONS root 864691135479404742, a proofread L5NP neuron in mouse V1, with detected incoming and outgoing synapses. — One proofread mouse V1 neuron. 4,738 skeleton nodes and 2,056 detected synapses, shown as a 2D projection of measured data.

Root 864691135479404742 · materialization 1926 · not a whole-brain reconstruction · not a procedural scientific visualization.

Scroll to trace the workMouse · fly · algae · cells

01 / What we build

Three scales.
One discipline.

Connectomics, cultivation and single-cell observation are different questions. They share one requirement: make the evidence, the limits and the next test visible.

Projection of a measured MICrONS mouse neuron skeleton with its detected synapses.

NeuroML

Connectomics / mouse + fly

A scientific environment for neuron records, morphology and connectivity built from versioned public datasets. The first slice is one proofread MICrONS neuron; the whole brain is not claimed.

Live recordPinned · materialization 1926 02

Algaephyte

Cultivation / sensing + models

A proposed cultivation instrument that brings sensors, cameras and growth models into one clearer view of a changing culture. Illustrative scene: a proposed instrument, not a deployed instrument.

Research conceptIn development 03

Cyanoflow

Single cells / microfluidics

A proposed way to separate, photograph and follow individual cells so their differences are not lost in an average. Research design goals, not validated hardware performance.

Research conceptIn development

02 / The standard

The unit of trust is a source,
not a screenshot.

A claim without a record is only a rendering.

Orr Biologicals is built around provenance. The current NeuroML slice reads a proofread MICrONS neuron at a pinned materialization, carries its skeleton hash and synapse table, and says plainly that one neuron is not a whole-brain reconstruction.

We keep measured observations, curated metadata, computational models and predictions in separate evidence classes. These are research concepts in development; when a value is missing, the interface says DATA UNAVAILABLE rather than estimating a number and presenting it as biology.

Inspect the real neuron record

1Verified neuronProofread MICrONS root 864691135479404742

2,056Detected synapses1,171 outgoing · 885 incoming at version 1926

4,738Skeleton nodes4,737 edges · 9,682.3 µm modelled length

03 / How we work

Research is a
chain of custody.

The platform is a record of what was measured, what was computed and what remains unknown. That distinction is part of the product, not a disclaimer added at the end.

Start with the source.

Dataset, version, query, table and retrieval time precede interpretation. A root id is not portable across versions without a mapping.

Separate observation from inference.

Skeletons and detected synapses are observations from an automated pipeline. Curated labels and model predictions retain their own evidence state.

Publish the limit with the result.

An automated synapse detector is not a complete manual reconstruction. A model is not a measurement. A page that hides either is not finished.

04 / The Journal

Notes from
the work.

Long-form notes on cultivation, imaging, connectomics and the engineering choices behind the tools. Research notes are not peer-reviewed publications.

Modeling a living systemResearch note

Can a model help us understand a culture?

What a digital version of a growing system can tell us, and where real observations still matter most.

Read the note

A closer look at individual cellsHow tiny liquid channels help researchers study cells separately.

What can a camera really tell us?The promise, and the limits, of looking for change in images.

What shapes the way algae grow?Nutrients, light and the assumptions inside a growth model.

Browse the JournalAll notes, organized by research area.

05 / Open by design

Built in the open.
Reviewed in public.

Source code, schemas, provenance and limitations belong with the result. The NeuroML page is source-linkable today; the public API is an engineering commitment, not a live endpoint we pretend exists.

Developer notes Research approach

GET /neuroML/data/neuron.json
200 source-linked record
schema neuroml.microns-neuron.v1
evidence Verified observation
state one neuron / not a whole brain

Provenance before prose
Versioned dataset identity
Unavailable is a valid answer
Code and limits together

Support independent biological research.
Your voluntary contribution supports computational biology tools, scientific visualization and open research resources.

clumsyparsnip913@walletofsatoshi.com

About contributions ↗

06 / Correspondence

What are you
curious about?

Have a research question, a dataset to compare or a different way of seeing things? This form opens an email draft; you decide when to send it.

Open tools for biological discovery.

Three scales.One discipline.