SerialEM Data Collection

A hands-on microscope operation for SerialEM SPA Data Collection. Prerequisite: SerialEM Introductory Training Workshop or equivalent.

Clock

Remote

Clock

4 Days

User

6-8
Trainees

Sun

Morning
Practical

Afternoon

Afternoon
Practical

Afternoon

No Cost

Dates:  September 14-17th, 2026

Registration: FREE

Who: PNCC Awarded General Access Proposal members only


The Pacific Northwest Center for Cryo-EM (PNCC) would like to offer a four-day remote training workshop for 6-8 trainees on SerialEM data collection at PNCC from Sept 14-17, 2026. This course is focused on training users to independently operate the microscope and collect data for single particle studies. This is an advanced course where students are required to have basic understanding of SerialEM and Microscope UI. Students are required to take the prerequisite course SerialEM Screening workshop prior to applying or have equivalent training.


APPLY HERE


NOTE: Workshop dates will be determined when enough suitable applicants have applied. To maximize impact, PNCC prefers to train one lab member per group with the intention that member further trains others in their group. Preference of trainees is given to individuals who have research projects ready for cryo-EM investigations and have background in structural biology. Application closes August 10th, 2026 at 10am (Pacific). 

 

Agenda

Each day includes a combination of presentations, demonstrations, and hands-on practice. Workshop runs from 9am to 5pm (Pacific) each day.

Day 1

  • Welcome & Workshop Overview
  • Introduction to the SerialEM Data Collection Workflow
  • Hands-On Learning: Setting Up the Beam

Day 2

  • Introduction to the Gatan Imaging Filter BioContinuum
  • Introduction to Gain Collection on the K3 Direct Electron Detector
  • Hands-On Learning: Beam and Instrument Setup

Day 3

  • Introduction to Montaging, Multishot, and Target Selection
  • Introduction to Camera and Scripts
  • Hands-On Learning: Full Workflow

Day 4

  • Review of Workflow
  • Introduction to Parameter Selection
  • Preparation for Merit Badge Evaluation

Day 5

  • SerialEM Data Collection Merit Badge Evaluation
  • Introduction to On-The-Fly Processing
  • Workshop Wrap-Up and Next Steps