𧩠Why a Workstation is Essential for SPA
β A Practical Approach to Cryo-EM and Negative-stain EM Data
1) What is Single-Particle Analysis (SPA)?
SPA reconstructs 3D structures from many 2D particle images acquired by EM. The same computational principles apply to both Cryo-EM and Negative-stain EM.
- Cryo-EM SPA: often uses hundreds of thousands of particle images; can reach near-atomic resolutions.
- Negative-stain SPA: typically uses thousands of particle images; suitable for medium-to-low resolution and early screening.
Standard steps:
- Motion Correction β only when data are acquired as movies. Some microscopes/cameras (especially older ones) do not support this.
- CTF Estimation
- Particle Picking
- 2D Classification
- 3D Reconstruction & Refinement
2) Cryo-EM vs Negative-stain EM (from SPA perspective)
| Item | Cryo-EM | Negative-stain EM |
|---|---|---|
| Sample state | Particles in vitreous ice | Particles on thin carbon film, stained with heavy-metal salts (e.g., uranyl acetate, phosphotungstic acid) |
| Data size | Hundreds of GB to TBs | Hundreds of MB to a few GBs |
| Output noise level | Relatively high (low contrast) | Lower (staining increases contrast) |
| Resolution range | Up to near-atomic | Medium-to-low (β10β20 Γ ) |
| Purpose | High-resolution structure | Early screening & QC |
Note: Common negative stains include uranyl acetate (UA) and phosphotungstic acid (PTA).
3) Why you need a workstation
SPA workloads stress GPU, CPU, RAM, and storage I/O. Cryo-EM often requires cloud-grade resources:
- CPU: β₯64 cores
- RAM: β₯512 GB
- GPU: multiple high-VRAM cards
- Scratch SSD: β₯1 TB
- Storage: tens of TBs
This is expensive for individuals.
4) A realistic alternative β a training-grade workstation
This series targets a laptop/desktop-class workstation capable of Negative-stain processing and small Cryo-EM datasets for learning.
My current setup:
- GPU: NVIDIA Quadro RTX 5000 (16 GB)
- CPU: 12 cores (24 threads)
- RAM: 64 GB
- Main Storage: 1 TB NVMe
- External: 4 TB SSD
With this, I run RELION and CryoSPARC side-by-side. Itβs ideal for Negative-stain analysis and can process small Cryo-EM datasets (hundreds of GB)βwith clear limits for very large projects.
In short, this workstation lets you:
- install and operate real SPA software,
- iterate the full workflow on small datasets,
- internalize Cryo-EM processing fundamentals.
5) Takeaway
A modest workstation provides the fastest feedback loop to learn SPA. Negative-stain data are small and high-contrast, making them perfect for practice. Upcoming posts will cover hardware selection β OS/CUDA setup β integrated CryoSPARC/RELION installation step by step.
Summary
- SPA applies to both Cryo-EM and Negative-stain EM
- Motion correction requires movie-capable cameras
- Cryo-EM needs cloud-scale resources; Negative-stain fits small workstations
- An RTX 5000/64 GB/1 TB NVMe/4 TB external setup can handle training and small datasets