Title: EM Image Processing and Data Analysis  
Author: Masaaki Kuwajima Mar 21, 2016
Last Changed by: Michael A Chirillo Feb 13, 2024
Tiny Link: (useful for email) https://wikis.utexas.edu/x/oaQEC
Export As: Word · PDF  
Incoming Links
KH Lab Wiki (1)
    Home page: KH Lab Wiki Home
Hierarchy
Parent Page
    Home page: KH Lab Wiki Home
Children (7)
    Page: Legacy Reconstruct Protocols
    Page: Identify/Trace EM structures
    Page: Ancillary Programs and Tools
    Page: Section Thickness
    Page: Unbiased 3D stereology
    Page: Dendrite Analysis Spreadsheets
    Page: Deprecated Protocols
Labels
There are no labels assigned to this page.
Page Permissions
Page restrictions:
  • Only users in group khlab-senior can edit this page. (set by Masaaki Kuwajima at Nov 27, 2017 09:08)
  • Only users in group khlab-super can edit this page. (set by Masaaki Kuwajima at Nov 28, 2017 04:26)
  • Only users in group khlab-user can edit this page. (set by Masaaki Kuwajima at Nov 27, 2017 09:08)
  • Only ae2577 can edit this page. (set by Anna-Maria Else Escherich at Oct 08, 2019 07:13)
  • Only mk23564 can edit this page. (set by Masaaki Kuwajima at Nov 27, 2017 09:08)
Recent Changes
Time Editor  
Feb 13, 2024 02:22 Michael A Chirillo View Changes
Jan 30, 2024 10:22 Masaaki Kuwajima View Changes
Jan 30, 2024 10:22 Masaaki Kuwajima View Changes
Dec 05, 2023 16:24 Masaaki Kuwajima View Changes
Dec 05, 2023 16:24 Masaaki Kuwajima  
Outgoing Links
External Links (21)
    https://doi.org/10.1523/ENEURO.0205-19.2019
    https://wikis.utexas.edu/display/khlab/Section+Thickness
    https://neuronline.sfn.org/scientific-research/ask-an-exper…
    fiji.sc/
    https://www.jneurosci.org/content/40/21/4076
    https://www.eneuro.org/content/6/4/ENEURO.0205-19.2019
    https://doi.org/10.3352/jeehp.2021.18.17
    https://elifesciences.org/content/4/e10778
    bionetgen.org/index.php/CellBlender_Tutorial
    www.bulkrenameutility.co.uk/Main_Intro.php
    https://www.jneurosci.org/collection/experimental-design-ed…
    https://www.psychologie.hhu.de/arbeitsgruppen/allgemeine-ps…
    https://synapseweb.clm.utexas.edu/atlas
    https://github.com/mcellteam/cellblender
    https://stats.oarc.ucla.edu/other/mult-pkg/seminars/intro-p…
    https://www.nature.com/collections/qghhqm
    synapseweb.clm.utexas.edu/software-0
    https://neuromorph.epfl.ch/
    imagej.net/TrakEM2
    https://synapseweb.clm.utexas.edu/tutorials
    www.mcell.org/tutorials/
KH Lab Wiki (30)     Page: Interacting with 3DEM.org
    Page: Tracing Z-Lengths
    Page: TrakEM2 (elastic alignment)
    Page: Starting a New Series
    Page: Image acquisition and processing workflow (Harris lab specific)
    Page: CellBlender and Neuropil Tools
    Page: STATISTICA
    Page: PyReconstruct user guide
    Page: SER and Spine Apparatus Identification
    Page: Editing Trace Palette Template
    Page: Counting or Tracing Mictotubules
    Page: Ribosome Identification
    Page: Unbiased 3D stereology
    Page: Neuropil Tools for Blender
    Page: Tracing synapses
    Page: Making Box and Whisker Plots in Excel
    Page: EM Image Processing and Data Analysis
    Page: Dendrite Analysis Spreadsheets
    Page: Grey Wall Tracing
    Page: Stamping Dendritic Protrusions
    Page: Identifying Symmetric and Asymmetric Synapses in the Hippocampus (CA1 Stratum Radiatum)
    Page: Using Neuropil Tool (CellBlender) to analyze axons
    Page: Exporting quantitative data
    Page: Deprecated Protocols
    Page: Series Code Assignment
    Page: Stamping Small Synaptic Vesicles
    Page: AlignEM-SWiFT (image alignment)
    Page: Calibration Error Correction Strategy
    Page: SDSA Analysis
    Page: Reconstruct Color Scheme