Tomogram Subvolume Alignment and Averaging with PEET

University of Colorado, Boulder


Description of PEET
Publications
PEET Discussion Group
Documentation for PEET
Submitting a Bug or Requesting Help
Download

Description of PEET

PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. It seeks the optimal alignment of each particle against a reference volume through several iterations. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET uses the parallel processing framework within IMOD, so that the lengthy computations can be distributed to multiple cores on one computer, to a set of linked workstations, or to a cluster. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

Publications

PEET was first applied for averaging axonemes and its methods were described in Nicastro et al 2006. Many new features have since been added, including clustering / classification as described in Heumann et al 2011. Please cite these papers if you use PEET in your research.

Many, more recent references with links to BibTex formatted citations and open-access content can be found in the PEET Biblography. This bibliography is not exhaustive; if we've inadvertently omitted a publication of yours using PEET, and you'd like us to add it, please let us know.

PEET Discussion Group

The PEET discussion group provides a forum for registered users to ask and answer questions, to share their experiences, and to receive notification of new releases and other PEET news. Digests and posting via email (i.e. list server functionality) are provided. Additional capabilities, including browsable / searchable archives are available through a web interface. Access to the web interface requires a Google login profile, which must be associated with the email address at which you wish to be contacted. (Non Gmail addresses can be used with a Google login, with or without a Gmail address. See the Email section of your Google Account settings). The group is not moderated, but joining requires approval.

To subscribe or visit the group via the web interface please visit PEET-LIST and sign in with your Google account. If you do not have and are not willing to create a Google login and are satisfied with email only access, you can also request membership by sending an email to peet-list+subscribe@colorado.edu. When you receive a confirmation email, simply reply to it (rather than pressing "Join This Group") to submit your request. If neither of the above methods works for you, you can also request to be manually added to the group by sending an email to john.heumann@colorado.edu.

After your request is approved, you will be added to the group and will receive a confirmation email with additional instructions. Once subscribed, if you have a Google account we request that you edit your membership settings for this group via the web interface so that your display name is your real name. To post to the forum you can either use the web interface or simply email your posting to peet-list@colorado.edu

To cancel your subscription, use the web interface or send an email to peet-list+unsubscribe@colorado.edu.

When replying to a previous posting via email, you will have the option to reply to the sender or to the list. Private replies may be appropriate for preliminary discussions, but please sure to post any final solutions or workarounds to the group so they will be available to everyone.

Documentation for PEET

Man pages are available in both ASCII and html formats for each of the programs comprising PEET. These pages ship with PEET, and can also be viewed online here, or downloaded (but not viewed online) from the "man" subdirectory of https://bio3d.colorado.edu/ftp/PEET/. Installation instructions are also included with PEET in file INSTALL.TXT. A guide for running PEET through the eTomo graphical user interface can be found at https://bio3d.colorado.edu/PEET/PEETmanual.html. If you use Alpha, Beta, or nightly versions of Imod, a more recent copy including newer features can be found here. The guide is also distributed with IMOD and can be opened from the eTomo Help menu once PEET has been installed. A set of introductory tutorials can be downloaded from https://bio3d.colorado.edu/ftp/PEET/tutorials/ or viewed on our YouTube channel at https://www.youtube.com/BL3DEMC. The associated sample data sets can be downloaded from https://bio3d.colorado.edu/ftp/PEET/sampleDatasets/. Materials from a more advanced IMOD / PEET workshop held at Rocky Mountain Labs June 26-30, 2017 can be found at https://bio3d.colorado.edu/RML_2017/2017_IMOD_PEET_Workshop/index.htm. A description of near-atomic resolution subtomogram averaging on a 5 tomogram subset of EMPIAR-10164 can be found at https://bio3d.colorado.edu/PEET/HiResSTATutorial.pdf.

Submitting a Bug or Requesting Help

Defect submissions and requests for help are always welcome. While the PEET Discussion Group is the main venue for support, requests can also be emailed directly to to john.heumann@colorado.edu. We reserve the right to forward direct requests (after anonymization, if requested) to the discussion group if we feel they are of broader interest.

We try to provide excellent responsiveness and customer service. You can help considerably by making sure your requests are clear and complete. Before submitting, please consider the following. 1) Have you updated to the most recent supported versions of PEET and IMOD and verified that the problem still exists there? If not, please do so before submitting. 2) Please be as explicit as possible. Describe exactly what you were doing, what the problem you encountered was, and, if possible, how to reproduce it. At a minimum, always include a description of the hardware you are running on, the operating system name and version, and both PEET and IMOD versions.

Ideally, attach or upload to the discussion group a tomosnapshot (from eTomo, press File->Run Tomosnapshot) taken in the PEET project directory immediately after the error occured. Screen shots can be included if desired, but are rarely helpful; a tomosnapshot is much more likely to contain the necessary information.