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