Manual vs. automatic particle picking

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Manual vs. automatic particle picking

As you learn very quickly, picking particles from your EM micrographs may become a slow step for your project if you are only using manual particle picking. This will make you consider automatic picking using Signature (or semi-automated using EMAN2 SWARM.

When should I use automatic particle picking?

Automatic particle picking is the most powerful when each micrograph in your dataset contains a homogenous spread of single particles. This is because automatic particle picking will pick nearly all features in your images, which may include:

• Aggregates
• Stain/ice crystals
• Smaller/large proteins in your images

This means that you need to check what Signature and SWARM in EMAN2 pick from your micrographs. If it it is picking >10% of features that are NOT your particles, it will become increasingly difficult to remove these 'bad' particles from your particle stack.

When should I use manual particle picking?

Manual particle picking is the most effective when you have a small dataset, or if your grid is very heterogenous with stain/ice crystals or aggregates. When this 'junk' interferes with the automated picking AND you want to see what results you can achieve by analyzing the isolated particles in the images.

Ultimately, manual picking should only be used for preliminary analyses. Once you are ready for 3D analysis and cryo-EM, you will need to have automated particle picking routines.