Cryo-EM & Cryo-ET
Data Processing Consulting
I process cryo-EM and cryo-ET data remotely for structural biology groups: reconstruction, particle picking, tomogram segmentation, sub-tomogram averaging, and custom AI models trained on your own data.
I do every job myself: Ian Cooney, Ph.D. (Stanford; first-author Science and Nature Communications).
Or skip the form and email info@cryoemservices.com directly.
Free scoping. I reply within two business days with an approach and a fixed price, before you commit to anything.
- Processing project$2,000–5,000
End-to-end single-particle reconstruction or tomogram processing, from movies to a validated map or segmented volume.
- Custom AI model, trained on your data$20,000
One price for the outcome: a model that works on your data, whether that means adapting a published network or designing one from scratch. Delivered trained, validated, wired into your pipeline and documented, and you own it outright, with no licence and no per-use fees.
- Workstation installfrom $500
RELION, cryoSPARC and supporting tools built against your CUDA and driver versions, documented so your next student can rebuild it. Usually done within a day of access.
- Single reviewer request$600–1,500
One analysis reprocessed on your existing data, with the figure and the methods text written so you can edit it. Most are days rather than weeks.
Fixed price agreed before any work starts. If the job turns out to be smaller than quoted, the quote goes down.
Data Services
Remote work for university labs, research institutes and biotechnology companies.
Single Particle Cryo-EM
End-to-end data processing pipelines from raw movie alignment to high-resolution density maps. Expertise in motion correction, CTF estimation, particle picking, 2D classification, 3D ab-initio reconstruction, refinement, post-processing, and map sharpening in RELION and CryoSPARC.
Custom AI Model Training & Fine-Tuning
Deep-learning models trained or fine-tuned on your own data for segmentation, denoising, particle picking and classification, for the cases where published tools miss your features. You get the trained model, inference scripts and documentation, and you own it outright. See what I build and get a fixed quote.
Cryo-ET & Subtomogram Averaging
Tomogram reconstruction, alignment, and sub-tomogram averaging. Support for automated and manual filament/membrane tracking, particle picking (template matching and deep learning-based approaches), and subtomogram alignment/averaging using PyTom, Dynamo, or custom pipelines.
Software Installation & Setup
Remote installation and configuration of Cryo-EM and Cryo-ET software stacks on local workstations, GPU servers, or HPC clusters. Includes RELION, CryoSPARC, IMOD, AreTomo, Dynamo, EMAN2, cisTEM, MotionCor2/3, CTFFIND, and deep-learning tools (Topaz, crYOLO, MemBrain-seg). You or your IT handle the hardware and the base OS; I take it from the GPU driver up. See what I install and get a fixed quote.
Cryo-ET Segmentation & Analysis
Membrane and organelle segmentation of cryo-electron tomograms using deep learning (MemBrain-seg, Dragonfly, IMOD) and manual approaches. Quantitative analysis of segmented volumes including surface area measurements, curvature mapping, and spatial distribution statistics.
Custom Pipelines & Scripts
Custom script development (Python, Bash) to automate data ingestion, transfer, metadata collection, and processing jobs on local GPU workstations or high-performance computing (HPC) clusters.
Model Building, Refinement & Validation
Atomic model building into your density, real-space refinement, and validation to publication standard using Coot, ISOLDE and Phenix. Includes ligand fitting, geometry and clash resolution, and a validation report you can put straight into a manuscript.
PDB & EMDB Deposition Support
I prepare and submit your depositions: map and half-map packaging, metadata and processing provenance, FSC curves, and responses to validation queries from the annotators. This is the step most groups underestimate, and it usually sits between you and a submitted paper.
Figures & Movies for Publication
Publication and cover-quality figures and animations rendered in ChimeraX, including map and model overlays, conformational morphs, and tomogram fly-throughs. Delivered as layered, editable source files at journal resolution.
Reviewer Response Reprocessing
Reviewer asked for a different mask, an extra class, local refinement, or a resolution estimate you did not report? I turn those requests around on a revision deadline, and document exactly what changed so the rebuttal writes itself. Send me the reviewer comments.
National Center Access Proposals
NCCAT, PNCC and S²C² give away Titan Krios time for free, but only through a written proposal, and weak sample-justification is the usual reason they get turned down. I help you scope the request, present your screening evidence, and write the justification. See the funding finder for what each center currently offers.
Fellowship & Job Applications
Separate from my data work: review and coaching for PhD students and postdocs on fellowship applications (F31, F32, K99 and equivalents) and on academic job materials. I have written and won an NIH F31 and a Parkinson's Foundation postdoctoral fellowship. See what I look at.
Submit a Project Inquiry
Prefer email? Write to info@cryoemservices.com.
Why Work With Me on Cryo-EM Data Processing?
Cryo-EM data processing is one of the most technically demanding steps in structural biology. From motion correction and CTF estimation through particle picking, 2D/3D classification, and final refinement, each stage requires expertise to avoid resolution-limiting errors. I have taken my own projects through every one of those stages to published structures, listed below, and I process your data the same way.
For cryo-electron tomography (cryo-ET) projects, I cover tilt series alignment, tomogram reconstruction with AreTomo and IMOD, deep learning-based segmentation using MemBrain-seg and Dragonfly, and sub-tomogram averaging with Dynamo and PyTom. My postdoctoral research at Stanford uses FIB-SEM cryo-electron tomography, so this is my working field rather than a side offering.
I work remotely, for labs at universities, medical schools, national laboratories and biotech companies. Data transfer is handled securely via Globus, SFTP, or direct access to your institution's HPC cluster. Every deliverable includes a processing report with parameter logs, so the work is fully reproducible.
How Cryo-EM Consulting Works
Submit Your Project
Fill out the inquiry form above with your sample details, dataset size, and processing goals. I reply within two business days with a free project assessment.
Get a Custom Quote
I review your data and propose a processing strategy, timeline, and flat-rate price. No hourly billing surprises. You know the cost upfront.
Receive Your Results
I deliver publication-ready density maps, segmented tomograms, or configured software, with full processing reports and reproducible parameter logs.
Peer-Reviewed Track Record
The processing and model building behind this service is the same work that produced these papers. Every one is public, so you can judge the quality yourself rather than take my word for it.
Cdc48 segregase caught unfolding an authentic substrate
Single-particle cryo-EM of an endogenous substrate-engaged AAA+ unfoldase, from native complex isolation through reconstruction.
Cooney et al., Science 365, 502–505 (2019)
A full conformational pathway resolved by classification
Heterogeneous classification used to separate an entire range of functional states from one dataset, rather than reporting a single consensus map.
Cooney et al., Nature Communications 15, 7505 (2024)
Active conformation of a human unfoldase complex
Protein purification and data processing contribution to a collaborative structure of the p97–p47 complex.
Xu, Han, Cooney et al., Nature Communications 13, 2640 (2022)
Published sample-preparation protocol
A peer-reviewed workflow for isolating native complexes from lysate intact enough for cryo-EM, useful when your target will not survive conventional purification.
Cooney et al., Bio-protocol 13(2) (2023)
A good fit if
- You have collected movies or tilt series and need them turned into a map or tomogram
- You have a map and need a model built, refined and validated
- You are facing a revision deadline and need reprocessing done quickly
- You need a deposition prepared and shepherded through validation
- Your group has microscope access but no dedicated processing expertise
Not a fit if
- You need wet-lab work: expression, purification or grid freezing done for you
- You need microscope time itself. Use the facility directory or a national center instead
- Your dataset does not exist yet and you want the whole project outsourced end to end
- You need hardware repair or on-site work. Everything I do is remote, starting from a machine that boots with its operating system and network
Frequently Asked Questions
What cryo-EM data processing services do you offer?
I offer end-to-end single particle cryo-EM processing (motion correction, CTF estimation, particle picking, 2D/3D classification, refinement, and map sharpening), cryo-ET reconstruction and sub-tomogram averaging, tomogram segmentation using deep learning, cryo-EM software installation and configuration on workstations and HPC clusters, and custom pipeline development.
How much does cryo-EM data processing consulting cost?
Single particle processing projects typically run $2,000–5,000 for straightforward datasets. Software installation starts at $500, clusters $1,500–3,000. Reviewer-response reprocessing is $600–1,500 per request. Custom AI models trained on your own data are $20,000, whether the task needs an existing model adapted or a new one built. Cryo-ET and sub-tomogram averaging are quoted individually on the number of tomograms and complexity. Fixed price agreed before any work starts. If the job turns out to be smaller than quoted, the quote goes down. Scoping is free.
What software do you use for cryo-EM processing?
I work in all the major cryo-EM and cryo-ET packages, including cryoSPARC, RELION, IMOD, AreTomo, Dynamo, PyTom, EMAN2, cisTEM, MotionCor2/3, CTFFIND, Topaz, crYOLO and MemBrain-seg. I can work with your preferred tools or recommend a pipeline for your project.
Can you process data remotely?
Yes. All of my work is remote: I take your data over secure transfer (Globus, SFTP, cloud storage) or work on your institution's HPC cluster through VPN. I do not do hardware repair or on-site work; for software installation, you or your IT keep the machine booting with its operating system and network, and I take it from the GPU driver and CUDA up.
What is the typical turnaround time?
For single particle processing, expect 1–3 weeks depending on dataset size and sample complexity. Cryo-ET segmentation and sub-tomogram averaging projects typically take 2–4 weeks. If you have a hard deadline, tell me; an expedited timeline may cost more, and I'll say so in the quote. Single-workstation installs are usually done within a day of access; cluster work is scoped individually.
Do you offer consulting for grant applications?
Yes. I can help draft cryo-EM methodology sections for NIH R01, R21, and other grant applications, including data processing workflow descriptions, computational resource justifications, and budget estimates for processing costs.
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