CryoSPARC: What It Is, How to Install It, First Workflow

CryoSPARC is software that turns raw cryo-electron microscopy (cryo-EM) images into a three-dimensional density map of a protein or other macromolecule. This guide is for structural biologists, core-facility staff and research computing teams who need to know what it does, how to obtain and install it, what a first processing run looks like, and where the results go afterwards. Facts below come from the CryoSPARC guide at guide.cryosparc.com, the EMBL-EBI EMDB site, the RELION documentation and the peer-reviewed literature, read on 2026-11-07.

What is CryoSPARC and what is it used for in research?

CryoSPARC is a software package for processing single-particle cryo-EM data. It was introduced by Punjani, Rubinstein, Fleet and Brubaker in Nature Methods 14(3):290-296 (2017, doi:10.1038/nmeth.4169). The paper describes an approach that combines stochastic gradient descent with branch-and-bound maximum-likelihood optimisation and allows ab initio reconstruction, meaning a first 3D model can be built from the images without a prior structure. That 2017 paper is the reference to cite when you report use of the software.

In practice the program takes movies from an electron microscope, corrects beam-induced motion, estimates the contrast transfer function, picks and extracts particles, sorts them into 2D and 3D classes, and refines a final map. It runs as a web application on a master process, with GPU worker processes doing the computation.

What is a cryo-EM map?

A cryo-EM map is the three-dimensional density volume reconstructed from many two-dimensional images of frozen particles. It is the main result of a CryoSPARC refinement job. The EMDB (Electron Microscopy Data Bank, run by EMBL-EBI) describes itself as a public repository for cryogenic-sample electron microscopy volumes and representative tomograms of macromolecular complexes and subcellular structures, and lists single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging and electron crystallography among the techniques it holds. It listed 64,153 entries as of 4 November 2026. Raw image data can be deposited separately: see EMPIAR, the public image archive, and, for the atomic models built into maps, the Protein Data Bank.

What are the disadvantages of cryo-EM?

The software is rarely the first limit; sample preparation usually is. A 2018 review in Acta Crystallographica Section D (Drulyte et al., 74(6):560-571, doi:10.1107/S2059798318006496) states that for many single-particle projects major bottlenecks remain at the sample-preparation stage. It lists these specific problems:

• obtaining grids of sufficient quality can require careful optimisation of many variables;
• problems with the sample itself, such as buffer components and labile complexes;
• sample distribution, including concentration and affinity for the support film;
• preferred orientation of particles;
• poor reproducibility of grid making within and between batches.

For how specimen preparation limits attainable resolution in electron microscopy more generally, see transmission electron microscopy sample preparation and resolution. For a method that works from crystals instead of frozen particles, see X-ray crystallography.

How to access CryoSPARC (official source only)

According to the CryoSPARC guide, the software is free for non-profit academic use. You request a License ID through the form on the download page at cryosparc.com/download. For-profit use is licensed separately through Structura Biotechnology (contact address given in the guide: [email protected]). Many institutions run CryoSPARC on a shared cluster, in which case access is a matter of asking your facility for an account on its existing instance rather than installing it yourself.

How to install CryoSPARC

Requirements stated in the guide

• At least 15 GB of disk for the packages.
• An installation path of no more than 83 characters.
• Worker nodes need an NVIDIA GPU with driver 570.26 or newer (x86-64) or 580.65.06 or newer (ARM64); the master runs on x86-64 only.
• The master’s ports must not be directly reachable from the internet, and the filesystem holding the database must not fill up.
• The --cudapath option applies only to versions before v4.4.0.

Download

Set LICENSE_ID and VERSION, then:

curl -L "https://get.cryosparc.com/download/master-$VERSION/$LICENSE_ID" -o cryosparc_master.tar.gz
curl -L "https://get.cryosparc.com/download/worker-$VERSION/$LICENSE_ID" -o cryosparc_worker.tar.gz
tar -xf cryosparc_master.tar.gz cryosparc_master

Single workstation (master and worker together)

cd cryosparc_master
./install.sh --standalone --license $LICENSE_ID --worker_path <worker path> --ssdpath <ssd path> --initial_email <email> --initial_username "<user>" --initial_firstname "<given>" --initial_lastname "<surname>"

Optional flags include --port <n> and --initial_password <pw>. Then open http://<workstation_hostname>:<base_port_number> in a browser and sign in as the admin user you created. The guide’s examples use port 61000 for the master.

Separate master and worker (cluster setups)

# master
./install.sh --license $LICENSE_ID --hostname <master_hostname> --dbpath <db_path> --port <port_number>
./bin/cryosparcm start
cryosparcm user create --email ... --password ... --username ... --firstname ... --lastname ... --role admin

# worker
cd cryosparc_worker
./install.sh --license $LICENSE_ID
./bin/cryosparcw connect --master <master_hostname> --worker <worker_hostname> --port <port_num>

For a scheduler-managed cluster the guide uses cryosparcm cluster connect with a cluster_info.json and a cluster_script.sh. Other install flags (--insecure, --allowroot, --yes) exist; the guide’s installation page lists them for each version.

A first workflow: the introductory tutorial, step by step

CryoSPARC’s own introductory tutorial (v4.0 and later) processes a 20-movie subset of EMPIAR-10025, the T20S proteasome. Get the data on the master with cryosparcm downloadtest and extract it with tar xvf. In the web interface, press New Project, create a workspace, then build jobs in this order. Import values for this dataset are pixel size 0.6575 Å, 300 kV, Cs 2.7 mm, total dose 53 e/Ų.

1. Import Movies
2. Patch Motion Correction
3. Patch CTF Estimation
4. Micrograph Denoiser (v4.5 and later, optional)
5. Blob Picker (particle diameter 100-200 Å)
6. Micrograph Junk Detector (v4.7 and later, optional) and Inspect Particle Picks
7. Extract From Micrographs (box size 440; about 11,129 particles)
8. 2D Classification (50 classes), then Select 2D Classes
9. Template Picker (diameter 190 Å), then Inspect, Extract, 2D Classification and Select 2D Classes again
10. Ab-Initio Reconstruction
11. Homogeneous Refinement (D7 symmetry for this specimen)
12. Volume Tools / masking and Validation (FSC); Sharpening Tools is optional

The Tree View (flowchart icon) shows how jobs connect. Job names and version tags above are from the current guide; menu items can change between releases, so follow the guide for the version you installed.

Output and how to read it

Stage	Job	What comes out
Preprocessing	Patch Motion Correction, Patch CTF Estimation	Motion-corrected micrographs and per-micrograph CTF estimates
Picking	Blob Picker, Template Picker, Inspect Particle Picks	Particle picks
Extraction	Extract From Micrographs	Boxed particle images
2D	2D Classification, Select 2D Classes	Class averages and the subset of particles you keep
3D	Ab-Initio Reconstruction, Homogeneous Refinement	Initial volume, then a refined map (map_sharp) with gold-standard FSC (GSFSC) plots

The final map_sharp volume can be downloaded from the refinement job’s Outputs tab. Resolution is read from the FSC curves. A map intended for publication is then deposited, with the model, as described in the EMDB and PDB guides linked above.

Troubleshooting installation

• Installer fails or paths break: check that the install path is 83 characters or fewer.
• GPU not usable by the worker: compare the NVIDIA driver with the minimum above (570.26 on x86-64, 580.65.06 on ARM64).
• Browser cannot reach the interface: confirm the hostname and base port you passed to the installer, and that the master was started with cryosparcm start.
• Installing as root: the installer needs the --allowroot flag.
• Database problems: the guide warns that the database filesystem must not fill up.

Free alternatives

Software	What the official documentation says
RELION	Cryo-EM structure determination software using an empirical Bayesian approach, developed in Sjors Scheres’s group at the MRC Laboratory of Molecular Biology. Distributed under a GNU General Public License; the documentation says anyone, including commercial users, can download, use and modify it for free.

The RELION documentation asks users to cite the project’s papers; see its publications page for the reference that matches the version you used.

Frequently asked questions

What is CryoSPARC?

Software for processing single-particle cryo-EM data into 3D maps, described in Punjani et al., Nature Methods 2017. It is free for non-profit academic use under a licence requested from the vendor.

How do I access CryoSPARC?

Request a License ID at cryosparc.com/download for academic use and install it with the commands above, or ask your institution whether it already runs a shared instance. For-profit licensing goes through Structura Biotechnology.

What is a cryo-EM map?

The 3D density volume reconstructed from particle images; public maps are archived in EMDB.

What are the disadvantages of cryo-EM?

Sample and grid preparation is a common bottleneck, including preferred orientation and poor reproducibility between grid batches.

Is there a public CryoSPARC login page?

No single one. Each installation has its own web address (the hostname and base port set at install), and a facility may publish its own.

Sources (read 2026-11-07)

• CryoSPARC guide: How to download, install and configure; Introductory tutorial.
• Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA. cryoSPARC. Nat Methods 14(3):290-296, 2017. PubMed 28165473.
• EMBL-EBI, Electron Microscopy Data Bank.
• Drulyte I et al. Acta Cryst D 74(6):560-571, 2018. doi:10.1107/S2059798318006496.
• RELION documentation.