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CryoMaestro
Quick Start

The platform

The experiment, its data, and the people who explain it.

A browser-based research platform designed to connect acquisition, processing, scientific context, and review. Explore the research workspace, then follow the instrument and processing capabilities through a session.

Live microscope and camera functions depend on the instrument bridge and hardware validated for your deployment; processing and facility workflows can be adopted independently.

Quick Start Compare it to what you run today

Research workspace

From a session to a scientific explanation.

Source session and job context becomes a frozen snapshot, then versioned JSON, HTML, and PDF artifacts for review.
Current reporting scope: preserve a defined snapshot and verify its issued artifacts.

Current reporting scope

Review a result with its source context.

Session processing and 2D readiness reports use frozen snapshots, versioned JSON, HTML, and PDF artifacts, checksum verification, and project permission checks. They give a review a defined set of inputs and outputs.

In development

Build the story alongside the evidence.

The scientific notebook direction brings notes, images, charts, and spreadsheets into the experiment. Source-linked editing, saved revisions, and multi-user review remain integration work; these are not released Console features.

Concept notebook with reasoning, source-linked images, charts, and spreadsheets. Integration is in development.
Scientific notebook concept. These authoring blocks illustrate the product direction and are not released Console features.

Data governance means understanding where data came from, how it was processed, and which evidence supports a result. Availability of individual capabilities depends on deployment and qualification. Shared browser access does not grant instrument control.

01

Before the column

The grid has a history before it has an atlas.

A sample is frozen, boxed, shipped, logged, and booked onto an instrument long before anyone presses acquire. Most acquisition software meets the grid only after all of that has happened — and treats the preceding weeks as something to be re-typed.

Sample logistics

  • Shipments in and out, with arrival and condition records
  • Dewars → pucks → grid boxes → vial boxes → vials → grids
  • Samples and aliquots, linked to the grids made from them
  • Chain-of-custody events for every physical handoff

People and access

  • Projects, teams, people, and external customers
  • Instrument bookings with conflict-aware slot suggestions
  • Facilities and instrument registry across sites
  • Ownership and permissions that follow the project, not the folder
02

On the column

A collection plan you can read before you run it.

Targeting is treated as a compiler, not a wizard. You declare what you want collected; the system derives a versioned plan, expands it into exact microscope actions, and commits it as a durable queue. Planning and simulation support review; complete live multi-hole execution is still being qualified.

The acquisition compiler pipeline A declared target worklist is normalized, compiled into a versioned acquisition plan, expanded into exact microscope actions, and committed as a durable queue revision only after a pre-queue validation gate passes. Run events record what physically happened and are observed against the original declaration rather than rewriting it. declared derived executed Target worklist squares, clusters, holes, priorities — what you declare Normalized worklist hierarchy, eligibility, resolved template, skip reasons Acquisition plan order, cluster grouping, estimates, template snapshots Execution actions stage move, focus, drift, image shift, defocus, exposure Queue revision durable, ordered, versioned, status per action Run events physical observations and outcomes gate run events are observed against intent — they never rewrite it
Fig. 01 Targeting compiles rather than configures. Each arrow is a translation you can inspect, and nothing durable is written until validation passes.

Setup and calibration

  • Presets and preset alignment for atlas, grid, hole, focus and data states
  • Matrix calibration, pixel size, beam shift, movement and stage limits
  • Dose, apertures, detector references, grid types, storage targets
  • A software preflight that shows what is loaded and current for operator review

Targeting

  • Autoloader and cassette selection
  • Atlas montage with coverage preview and tile-level progress
  • Square detection, ranking, filtering, and stratified sampling
  • Hole finding with selectable algorithms and live detection tuning
  • Image-shift cluster preview validated against your maximum shift
  • Exposure, focus and drift template overlaid on a real hole image

Plan and queue

  • Worklist → normalized worklist → plan → actions → queue revision → run events
  • Template and target data snapshotted the moment a plan is committed
  • Every action carries dependencies, preconditions and a readable reason
  • A pre-queue gate for tool permissions, shift limits, and time/image/stage budgets
  • Advanced operators can inspect and edit the queue without the wizard
  • Route preview and status map, tied back to atlas coordinates
03

While the session runs

Quality that is allowed to change what happens next.

Drift rate, focus success, astigmatism, coma, CTF fit confidence, ice thickness — these are measurable while there is still time to act. Use these measurements to inform operator review. Automated responses require qualification for the specific instrument and workflow.

Live tuning

  • Autofocus by beam tilt and by stage
  • Automated stigmation and coma correction
  • Drift stabilization with measured rate and wait policy
  • Node, microscope and camera state exposed as an explicit control plane

Live quality

  • FFT and CTF fit as the movies arrive
  • Motion and drift trajectories per exposure
  • Ice thickness and contamination flags per hole
  • Continue, recheck, skip, pause or abort on bad statistics
  • Retries, skips and exceptions recorded as run events, never as edits to intent
04

After the frames land

Processing that still knows where the data came from.

Motion correction, CTF estimation, picking and classification run at session scale — and every result stays attached to the exposure, hole, square, atlas and grid it originated from. The session context is never flattened into filenames.

The canonical target hierarchy A session contains grids, which contain atlas tiles, square targets, square maps, hole targets, exposure targets, movies, and finally processing outputs. Every node keeps a stable identity and a parent, so a result can be traced back to the exact hole it came from. Session instrument, operator, output paths Grid sample, aliquot, custody, cassette slot Atlas tile low-mag montage, coverage Square target area, intensity, ice proxy, status Square map medium-mag parent image Hole target lattice, radius, thickness, cutoff reason Exposure target template, defocus, movement mode Movie frames, dose, path Processing outputs motion, CTF, particles, classes every result resolves back to the target that produced it
Fig. 02 One hierarchy, shared by acquisition and processing. This is why a class average can name the hole it came from, and why a hole can tell you why it was chosen.

Processing

  • Motion correction, CTF estimation, FFT, stack building
  • Template-based and model-based particle picking
  • 2D classification and class selection
  • Submit against one image or an entire session
  • Live progress streaming, with every result persisted

Looking at results

  • Result-specific views — Thon-ring sketches, drift traces, particle overlays
  • Hierarchy browser in column, gallery, table and list modes
  • Image viewer with metadata strip and overlay layers
  • Analysis workspaces, saved selections and labels
  • Jobs, runs, artifacts and pipeline health in one place
05

Across the facility

The unit of work is a facility, not a workstation.

Once sessions, instruments, nodes and people share one model, the questions a facility manager actually has become answerable — without exporting anything.

Analytics

  • Throughput over time, by instrument and by project
  • CTF and defocus distributions across sessions
  • Ice quality as a grid heatmap
  • GPU utilization and microscope KPI tables
  • Recent jobs, FSC overlays, and per-instrument comparison

Operations

  • Node discovery and fleet health across machines
  • System activity log and in-app messaging
  • Security, members, and team administration
  • Runs entirely on your own hardware — laptop, cluster, or cloud
06

Making it yours

Your method, as a first-class step.

The reason a platform outlives its authors is that reviewed methods can be added without exposing or changing the platform core. A typed extension contract defines inputs, outputs, resources, and result presentation.

Plugins

  • Reviewed extension contract → consistent forms and results
  • Consistent submission and result experience for every method
  • A plugin catalogue your facility controls

Workflows

  • Visual editor for source, compute, decision and transform steps
  • Sources: watched directories, URLs, EMPIAR accessions, S3, GCS, Azure, event streams, REST
  • Validation before a workflow is allowed to run
  • Workflows and presets stored as versioned, reviewable objects
  • A built-in assistant for navigating what ran and why

Why it holds together

Six chapters, one data model.

Nothing above is a separate module talking to another separate module over a shared drive. A grid, a session, a target, a job and a result are the same objects in all six sections — which is why a result can point back at the hole it came from, and why a hole can tell you why it was chosen.

Spans
Dewar to 2D classes
Runs on
Laptop, cluster, or cloud
Extends with
Reviewed typed contracts
Deployment
Private and controlled

Get started

See the whole chain on real data.

Open the bundled demo session and follow one grid through every chapter above, or install locally in five steps.

Open the demo Quick Start