Appion Workshop Series
The Appion Workshop Series is offered at intervals throughout the year. Check the Workshops and Courses on the SEMC website for the announcement of the next in the series, and to find the link to register for that workshop. Alternatively, please email memc [a] nysbc.org 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. The workshop is limited to 10 attendees. To learn the details of when this workshop begins and how to register click here.
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. The workshop is limited to 10 attendees. To learn the details of when this workshop begins and how to register click here.
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 specimens 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.
Attendees 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.
To learn the details of when this workshop begins and how to register, click here.
EM course [yearly]
Electron microscopy in combination with image analysis is increasingly powerful in producing 3D structures of individual molecules and large macromolecular complexes that are unapproachable by other methods. This course is focused on the concepts and theories behind electron microscopy and will be taught in a reverse classroom format based on Grant Jensen’s online course, Getting Started in Cryo-EM from Caltech. Students will be responsible for watching these online lectures prior to class. Each week guest lecturers and SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.
To learn the details of when this course begins and how to register, click here.