Archive Meta Data

Author(s)

Hans Jacob Teglbjærg Stephensen, Jon Sporring

Title

Rodent Neuronal Volume Annotations and Segmentations

Description

###############################################################################
#                                                                             #
# Derived datasets:                                                           #
# *) Manual annotations                                                       #
# *) Automatic segmentation                                                   #
# *) Cleaned segmentation                                                     #
#                                                                             #
# Authors: Hans Jacob Teglbjærg Stephensen, Jon Sporring                      #
# Contact: hast@di.ku.dk                                                      #
#                                                                             #
# Original FIB-SEM dataset authors Graham Knott and Marco Cantoni at EPFL     #
# Download link: https://www.epfl.ch/labs/cvlab/data/data-em/                 #
#                                                                             #
###############################################################################

Datasets:
*) sparse_manual_annotations
    Unsigned 8-bit unsigned integer mask
    Annotation type: Manual

    Lables:
        BACKGROUND_LABEL = 0
        MEMBRANE_LABEL = 1
        ACTIVE_ZONE_LABEL = 2
        MITOCHONDRIA_LABEL = 3
        ENDOPLASMIC_RETICULUM_LABEL = 4
        VESICLE_LABEL = 5
        NO_LABEL = 255

*) unet_segmentation_registered
    Unsigned 8-bit unsigned integer mask
    Annotation type: U-Net segmentation

    Lables:
        BACKGROUND_LABEL = 0
        MEMBRANE_LABEL = 1
        ACTIVE_ZONE_LABEL = 2
        MITOCHONDRIA_LABEL = 3
        ENDOPLASMIC_RETICULUM_LABEL = 4
        VESICLE_LABEL = 5

*) unet_segmentation_registered_cleaned
    Unsigned 8-bit unsigned integer mask
    Annotation type: Cleaned U-Net segmentation - cleaned in Avizo Amira

    Labels:
        BACKGROUND_LABEL = 0
        SYNAPSE_LABEL = 1
        MITOCHONDRIA_LABEL = 2
        VESICLE_LABEL = 3

*) synapse_labeling
    Unsigned 16-bit unsigned integer
    Annotation type: per synapse label. 365 synapses

    Labels:
        BACKGROUND_LABEL = 0
        SYNAPSE_1_LABEL = 1
        SYNAPSE_2_LABEL = 2
        ...
        SYNAPSE_365_LABEL = 365

*) drift_estimate.txt
    Per section registration in text format
    The estimate was perform using

    Drift Corrector Software:
        Stephensen, Hans Jacob Teglbjærg, Sune Darkner, and Jon Sporring.
        "Drift Corrector Software." (2019).
    Link: https://doi.org/10.17894/ucph.b61d5ca9-53df-4909-92ee-f8ee026e39bb

    Corresponding article:
        Stephensen, Hans Jacob Teglbjærg, Sune Darkner, and Jon Sporring.
        "Restoring drifted electron microscope volumes using synaptic vesicles
        at sub-pixel accuracy." Communications Biology 3.1 (2020): 1-7.
    Link: https://www.nature.com/articles/s42003-020-0809-4

    Each line has 5 values with the following meaning
    [cumulative drift axis 1] [cumulative drift axis 1] [N ellipsoids used for estimate] [drift axis 1] [drift axis 2]
    Line n corresponds to the values used for drift estimate between image section n-1 to n (0 indexing).