New user orientation [monthly]

New users are required to attend a group new user orientation session before use of the facility. We offer these 1-day orientation sessions at the beginning of each month from 9:30am to 3:00pm. The morning session covers the general laboratory policies and safety training, and the afternoon session includes a demonstration of TEM use and introduction to Leginon. New users are strongly encouraged to do some background reading before their first microscope session.

Following orientation, users may request time on the instruments in consultation with SEMC staff until they gain sufficient experience to receive sign off from staff to use the instruments independently.  Please note that each instrument requires individual training and sign off, which will be provided by SEMC staff on a one-on-one basis.  Separate training is required for 24 hour access; the initial sign off is only for use of equipment during normal business hours (9am to 5pm, Monday through Friday).

Please email Cathleen Castello at to inquire about future orientation session dates.
To view and/or download the slides presented at the Annual User Meeting, click here: Annual User Meeting Slides.

Appion Workshop Series

The Appion Workshop Series is offered at intervals throughout the year. Check the main page of our website for the announcement of the next in the series, and to find the link to register for that workshop. Alternatively, please email to inquire about future workshop dates.

Appion Workshop Part 1: 2D Analysis

The Appion Part 1 Workshop provides hands-on training for the Appion single-particle data processing workflow. Appion is a “pipeline” for processing and analysis of EM images; it is integrated with Leginon data acquisition, but can also be used stand-alone after uploading images or particle stacks. Topics include analyzing the quality of your data collection,correcting the CTF, generating and cleaning up stacks, and generating 2D class averages. An Appion Part 2 Workshop will be offered in the future to provide training for making initial models and doing 3D reconstructions. If you are interested in attending an Appion Part 1 Workshop, please email   The workshop is limited to 10 attendees.

Appion Workshop Part 2: Single Particle Analysis – 3D Reconstruction

This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and will focus on 3D initial models and refinement. If you are interested in attending an Appion Part 2 Workshop, please email The workshop is limited to 10 attendees.

Appion Workshop Part 3: Tomography

Tilt-series alignment is commonly performed by tracking fiducials in order to recover the three-dimensional structure and orientation of specimen in cryo-electron tomography, negative stain tomography, and tomography on plastic sections. However this approach is sometimes fraught with difficulty due to fiducial movement, fiducial aggregation, or the lack of fiducials in specimen such as FIB/SEM lamella.

In this workshop users will gain hands-on experience with a semi-automated implementation of Protomo into Appion. Protomo allows for fiducial-less alignment of tilt-series and refinement of specimen orientation on the grid through an iterative geometry refinement process. Appion-Protomo, which installs seamlessly with Appion, significantly reduces the effort and expertise required by the user to align fiducial-free tilt-series collected using any software package. All that is required is a stack of tilt images along with knowledge of their imaging conditions. Integrated within Appion-Protomo are pipelines for defocus estimation, CTF correction, and dose compensation, along with multiple reconstruction methods.

No previous experience in tilt-series alignment processing is required. Workshop attendees are encouraged to bring data in the form of tilt-series images or stacks for processing assistance.

Attedees are encouraged to sign up for the Dynamo workshop to learn how to extract and process subtomograms from their reconstructed tomograms.

Attendees should bring their own laptop in order to follow along during this hands-on workshop.

If you are interested in attending an Appion Part 3 Workshop, please email

Holey Gold Grid Workshop

This workshop will provide an overview of making holey gold films from holey carbon films supported on gold mesh. Holey gold films provide a stronger support film and reduce beam induced movement of the specimen. If you would like to attend this workshop, please email The workshop is limited to 6 attendees.

EM course [yearly]

SEMC’s “reverse classroom” style winter course is in session! Attendance has been high, and in the most recent class our students made ice cream with liquid nitrogen, one of the key components of sample preparation.

The course is based on an online video class taught by Grant Jensen.  Students watch these lectures prior to a formal 90 minute class that meets once per week for follow up materials and discussion.  Class dates and a detailed syllabus can be found on our website.