The first Appion workshops cycle of 2018


The Appion Workshop Series is offered at intervals throughout the year. These processing workshops are focused on helping users actively collecting data at the center.

Appion Workshop Part 1: 2D Analysis 

Tuesday, January 30th 

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. The workshop is limited to 10 attendees.


If you are interested in attending this Appion Part 1 Workshop register here:

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

Thursday, March 8th 

This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and will focus on 3D initial models and refinement. The workshop is limited to 10 attendees.


If you are interested in attending this Appion Part 2 Workshop register here:

Appion Workshop Part 3: Tomography   

Thursday, March 29th 

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 expertice 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 this Appion Part 3 Workshop register here::

2018-10-02T18:39:29+00:00January 25th, 2018|Uncategorized|