Pre-pro is a fast pre-processor for single-particle cryo-EM by enhancing 2D classification.

2D classification plays a pivotal role in analyzing single particle cryo-electron microscopy images. Here, we introduce a simple and loss-less pre-processor that incorporates a fast dimension-reduction (2SDR) de-noiser to enhance 2D classification. By implementing this 2SDR pre-processor prior to a representative classification algorithm like RELION and ISAC, we compare the performances with and without the pre-processor. Tests on multiple cryo-EM experimental datasets show the pre-processor can make classification faster, improve yield of good particles and increase the number of class-average images to generate better initial models. Testing on the nanodisc-embedded TRPV1 dataset with high heterogeneity using a 3D reconstruction workflow with an initial model from class-average images highlights the pre-processor improves the final resolution to 2.82 Å, close to 0.9 Nyquist. Those findings and analyses suggest the 2SDR pre-processor, of minimal cost, is widely applicable for boosting 2D classification, while its generalization to accommodate neural network de-noisers is envisioned.