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Library Digital Collections

Microscopy product ID: 3684

Component

2D Image

Description

Zero degree tilt electron micrograph from a double tilt series of a spine synapse from the molecular layer of cerebellar cortex tissue prepared using a combination of conventional chemical fixation followed by high pressure freezing, imaged using intermediate voltage electron microscopy

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Full resolution data file

File Size
  • 11.8 GB
File Format
  • TAR
Description

Tar file containing original digitized TIFF images (in folder marked A and B), IMOD files (*com, *log, st, preali, fid, rawtlt,...), and TxBR files (*mat, *txt, preali, rawtlt, fid, ...) of high pressure frozen Cerebellar tissue, showing post synaptic density. Note total file size is ~ 11 Gb, so this will take a long time to download.

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Animation

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Description

Aligned tilt series (one of two orthogonal tilt series from a double tilt tomogram) of a spine synapse from the molecular layer of cerebellar cortex tissue prepared using a combination of conventional chemical fixation followed by high pressure freezing, imaged using intermediate voltage electron microscopy.

Segmentation

Description

Segmentation of post synaptic density (PSD) using automatic segmentation

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Full resolution data file

File Size
  • 361 MB
File Format
  • SITX
Description

Sitx (zipped) archive of segmentation files generated by Amira (.hx, .am, surf) of the post synaptic density. Also included are animation files showing the surfaced PSD (PSDamira_surface_rot_noimage2.mpg) and a the surfaced PSD visualized along with computed slice through the tomographic volume (PSDamira_surface_rot.mpg).

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Reconstruction

Description

Single computed slice through a tomographic reconstruction of a spine synapse from the molecular layer of the cerebellar cortex from tissue that was prepared from a combination of chemical fixation and high pressure freezing. The contrast was adjusted and the image downsampled to 8 bits from the submitted data for display purposes.

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Full resolution data file

File Size
  • 7.54 GB
File Format
  • TAR
Description

Tar archive file containing TxBR combined (double tilt) tomographic volume of high pressure frozen cerebellar tissue in IMOD format. Two versions of the volume are included: the full resolution version HPFcere2_full.rec; a trimmed version HPFcere2_proj_trim.rec and a trimmed downsampled version HPFcere2_proj_trim_rot_trim_bin2.rec. Volume dimensions and scales given in CCDB are for the full resolution version. Also included are various animation files that show different types of projections through the volume. Total size of sitx file ~6 Gb.

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Animation

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Description

Animation of a tomographic reconstruction of a spine synapse from the molecular layer of the cerebellar cortex from tissue that was prepared from a combination of chemical fixation and high pressure freezing.

Full metadata

CCDB XML

File Size
  • 10.1 KB
File Format
  • XML
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Product description (pdf)

File Size
  • 269 KB
File Format
  • PDF
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Collection
Cite This Work

Ellisman, Mark H.; Sosinsky, Gina; Jones, Ying (2017). Microscopy product ID: 3684. In Cell Centered Database. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0542NDC

Creation Date
  • Experiment: 2006-08-17. Project: 2004-01-01.
Date Issued
  • 2017
Research Team Heads
Technical Details

Male. Strain: Sprague Dawley

Product type: DOUBLE TILT. Microscopy type: IVEM. Instrument: JEOL 4000 #1

Funding

NIH

Series
Scientific Name
Anatomy
Topic

Formats

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Language
  • No linguistic content; Not applicable
Related Resources

    Primary associated publication

    • Sosinsky GE, Crum J, Jones YZ, Lanman J, Smarr B, Terada M, Martone ME, Deerinck TJ, Johnson JE, Ellisman MH (2008). The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications. J Struct Biol, 161(3):359-371. PubMed: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2459253/; Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2007.09.002

    Other version

License

Creative Commons Attribution 4.0 International Public License

Rights Holder
  • UC Regents
Copyright

Under copyright (US)

Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.

Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.

Digital Object Made Available By

Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

Last Modified

2023-05-22