Karimi Ryan, Coupland Claire E, Rubinstein John L
Molecular Medicine Program, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Medical Biophysics, The University of Toronto, Toronto M5G 1L7, Canada.
Molecular Medicine Program, The Hospital for Sick Children, Toronto M5G 0A4, Canada.
J Struct Biol. 2024 Dec;216(4):108148. doi: 10.1016/j.jsb.2024.108148. Epub 2024 Oct 30.
Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of these vesicles can be challenging due to the strong signal contributed from the lipid bilayer. This challenge often requires iterative and laborious particle selection workflows to generate a dataset of high-quality particle images for subsequent analysis. Here we present Vesicle Picker, an open-source program built on the Segment Anything model. Vesicle Picker enables automatic identification of vesicles in cryo-EM micrographs with high recall and precision. It then exhaustively selects all potential particle locations, either at the perimeter or uniformly over the surface of the projection of the vesicle. The program is designed to interface with cryoSPARC, which performs both upstream micrograph processing and downstream single particle image analysis. We demonstrate Vesicle Picker's utility by determining a high-resolution map of the vacuolar-type ATPase from micrographs of native synaptic vesicles (SVs) and identifying an additional protein or protein complex in the SV membrane.
电子冷冻显微镜（cryo-EM）最近已能够确定嵌入脂质囊泡中的膜蛋白和蛋白质复合物的近原子分辨率结构。然而，由于脂质双层产生的强烈信号，从这些囊泡的电子显微照片中选择颗粒可能具有挑战性。这一挑战通常需要反复且费力的颗粒选择工作流程，以生成高质量颗粒图像数据集用于后续分析。在此，我们展示了Vesicle Picker，这是一个基于Segment Anything模型构建的开源程序。Vesicle Picker能够以高召回率和高精度自动识别冷冻电镜显微照片中的囊泡。然后，它会详尽地选择所有潜在的颗粒位置，这些位置要么在囊泡投影的周边，要么在其表面均匀分布。该程序旨在与cryoSPARC接口，cryoSPARC既执行上游显微照片处理，也执行下游单颗粒图像分析。我们通过从天然突触囊泡（SVs）的显微照片中确定液泡型ATP酶的高分辨率图谱，并在SV膜中识别出一种额外的蛋白质或蛋白质复合物，来证明Vesicle Picker的实用性。
