Electron Microscopy and Image Processing

I have a question about including astigmatism in the CTF correction of single particle reconstructions. Some people recommend not allowing astigmatism and just using an average value for the defocus in the calculations. The reason is that, unless the astigmatism is quite large, the additional defocus value and astigmatic angle that need to be determined add more error to the calculation rather than help restore high-resolution detail. Does anybody have experience with a data set that goes to high resolution?

Just out, this video publication in the Journal of Visualized Experiments by the lab of Peijun Zhang, which takes us through the reconstruction of a HIV-1 capsid tube assembly from freeze plunging to final reconstruction. Though the actual method may only be of interest to those working on helical projects, this may well be the first video publication on cryo-EM you watch!

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
Xin Meng, Gongpu Zhao, Peijun Zhang

Hi,

How do I align my 3d models before running diff map?

Thanks

Jimmy

This week-end I stumbled across a field of signal processing called Compressed Sensing, or sparse sampling.

These sampling and reconstruction techniques have been applied to real space and fourier space images, such as MRI, and CT scanning. It has led to people being able to reconstruct images when sampled with a single pixel. Turns out it's also starting to be applied to cryo-EM.

I have been trying to get my head around something which is probably quite simple today - and was thinking that someone on this forum could probably give me an answer!

Hi niko,
When calculating the difference map, if I apply a negative bfactor to both two 3D volumes before diffmap.exe, the diffmap.exe will run a longer time than no bfactor. So I read the source code, and found you used a VA04 function in diffmap.exe. I remember the VA04 is a Powell minimization subroutine. Can you tell me what you use the VA04 for? To scale the amplitude?
Thank you.
xueming

The single particle cryo-EM technique has become a universal approach for observing macromolecular assemblies at high resolution. It is now capable of imaging particles with high symmetry such as icosahedral viruses at near-atomic resolution. This achievement has been celebrated as a breakthrough and is the result of a number of technical advances, especially in image processing.

Niko,
I have downloaded your 'bfactor' program and would like to use it for filtering of the 3D map generated with EMAN.

I am new with your software. How to compile it for MacOS?

I would appreciate very much your help/advise.

Irina

In this paper, the authors used CLEM to image Sup35 fibril within yeast cells. As the authors say in their intro, until their study "there [was] no direct evidence for the presence of amyloid fibrils of Sup35 in [PSI+] cells". It is great to be able to image fibrils in vivo using EM.

Here is a link & the abstract:

In vivo evidence for the fibrillar structures of Sup35 prions in yeast cells.

Kawai-Noma S, Pack CG, Kojidani T, Asakawa H, Hiraoka Y, Kinjo M, Haraguchi T, Taguchi H, Hirata A.