Electron Tomograms and Microtubule Models from the publication Weber et al., 2011 [1]
Attached
are 5 electron tomograms, with their full microtubule model obtained by the combination of 4 manual tracings:
Copyright and Licenses, Condition
of Use
the
Electron Tomograms ©MPI-CBG 2011, hereinafter
"the
Tomograms", are MRC files generated using the IMOD Software [2], from semithin sections of C. elegans embryos in metaphase of mitotic division [1].
the
Software Microtubule
Tracing Package ©ZIB/MPI-CBG 2011, hereinafter
"the
Software". More information on the software can be found here:
the
Microtubule tracings ©ZIB/MPI-CBG 2011, hereinafter
"the
Models", were automatically calculated from the Tomograms, using the
Software and corrected with the editor tool of the Software and/or traced manually. Each model results from the combination of several manual tracings and/or automated segmentation and is therefore considered as ground truth.
the
Tomograms, the Models and the Software are collectively referred to
as “
Type Electron Tomogram Name in Publication Microtubule model
dual axis Box49-DT-6A-1-s3.rec DTHQ2
Box49-DT-6A-1-s3-superset.am
dual axis Box32L-DT-6A-2-s8.rec DTHQ1
Box32L-DT-6A-2-s8-superset.am
dual axis T0029-DT-4C-s2.rec DTMQ
T0029-DT-4C-s2-superset.am
Single axis T0038-ST-Nr1-3E-s6.rec STHQ
T0038-ST-Nr1-3E-s6-superset.am
Single axis Box49-ST-6A-1-s7.rec STLQ
Box49-ST-6A-1-s7-superset.am
And 3 dual-tilt tomograms where microtubule models were combined from automatic and manual tracings:
Type Electron Tomogram Name in Publication Microtubule model
dual axis T0133_2_3b_5_pos_.rec Tomogram X
T0133_2_3b_5_pos_superset.am
dual axis T0133_2_3b_4_pos_.rec Tomogram X
T0133_2_3b_4_pos_superset.am
dual axis T0133_1_1d_9_pos_.rec Tomogram X
T0133_1_1d_9_pos_superset.am
We consider the 8 models above as ground truth of microtubule segmentation for the respective electron tomograms.
http://www.zib.de/en/visual/software/MicrotubuleSeg.html
Max
Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108, 01307 Dresden, Germany
hereinafter referred to as “MPI-CBG“.
MPI-CBG holds the ownership on the Tomograms. ZIB and MPI-CBG hold all the ownership rights on the Software and the Models. ZIB and MPI-CBG grant you the non-exclusive, revocable right to use the Data free of charge, for the purpose of reproducing the procedure described in [1], for testing your own tracing algorithms, or to use the method for RESEARCH PURPOSES ONLY.
Users who publish their results based on any part of the Data (the Tomograms, the Models and/or the Software) must mention in their publication: the source of the Data, including the download website, a reference to publication [1], and the institutions ZIB and MPI-CBG. If a free license provided by VI was used, then VI must be mentioned, too.
Users of the data can communicate their remarks to ZIB (baum@zib.de) and MPI-CBG (verbavat@mpi-cbg.de).
NO COMMERCIAL USE, EXPLOITATION NOR DISTRIBUTION IS AUTHORIZED BY THIS LICENSE. IF SUCH USE OF THE SOFTWARE IS DESIRED, PLEASE CONTACT Hans-Christian Hege at ZIB (hege@zib.de).
THE SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL ZIB, MPI-CBG AND VI OR AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES, LOSS OF USE, DATA, OR PROFITS OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Publications
[1] Britta Weber, Garrett Greenan, Steffen Prohaska, Daniel Baum, Hans-Christian Hege,Thomas Müller-Reichert, Anthony A. Hyman, Jean-Marc Verbavatz, Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos, J. Struct. Biol., 2011, doi:10.1016/j.jsb.2011.12.004
[2] Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol. 1996 116(1):71-6.