
General Information

This readme file was generated on 2024-04-10 by Jacob Reiber and Dreson Russell.

This dataset involves the ultrastructural analysis of synaptic vesicle area, synaptic vesicle intervesicular distances, and synaptic cleft distance from male mice (n=4 PBS, n=4 PFF) bilaterally injected with PFF vs monomer for 3MPI timepoint. Ultrastructural analysis of synapses was performed using transmission electron microscopy (TEM).

File Overview:
All files represent different analyses from the same imaging dataset.

Data Specific Information
Files:

1. PSDlength_SVperPSDlength.csv

    - This file contains the length of PSD (postsynaptic density) and synaptic vesicles per PSD. 
    - Column headings:
        - animalno: The animal ID. IDs are conserved across all datasets.
        - psdlength: The measured PSD length in nm.
        - treatment: Designation for either pre-formed fibrils (PFF) or control (PBS) treatment groups.
            - 1: PBS (control)
            - 2: PFF
        - svperpsdlength: The observation of synaptic vesicles per PSD length.
        - synapseno: Synapses were annotated with a number to generate the corresponding data for each synapse.

2. SVarea_nearneighbor.csv

    - This file contains the nearest neighbor distances of synaptic vesicles and the area of individual synaptic vesicles.
    - Column headings:
        - animalno: The animal ID. IDs are conserved across all datasets.
        - synapseno: Synapses were annotated with a number to generate the corresponding data for each synapse.
        - nearestvesicle: The nearest neighbor distance of synaptic vesicles.
        - svarea: The measured area of individual synaptic vesicles.
        - treatment: Designation for either pre-formed fibrils (PFF) or control (PBS) treatment groups.
            - 1: PBS (control)
            - 2: PFF

3. synaptic_cleft_distance.csv

    - This file contains the measurements of synaptic cleft distance.
    - Column headings:
        - animalno: The animal ID. IDs are conserved across all datasets.
        - distance: The measured width of the synaptic cleft.
        - treatment: Designation for either pre-formed fibrils (PFF) or control (PBS) treatment groups.
            - 1: PBS (control)
            - 2: PFF
        - synapseno: Synapses were annotated with a number to generate the corresponding data for each synapse.

Methodology

Imaging was performed with an FEI Tecnai transmission electron microscope at an 80 kV accelerating voltage.
Digital images were acquired with an AMT NanoSprint15 MK2 camera (Advanced Microscopy Techniques, Woburn, MA).
Synapses were excluded from the analysis if they exhibited a poorly defined postsynaptic density (PSD), an intense PSD signal that obscured both membranes, a presynaptic terminal with fewer than 4 SVs, or if synapses were at the edge of the frame.
For the measurement of synaptic cleft width, the two edges of the PSD adjacent to the presynaptic terminal were determined, and the distance between the PSD and presynaptic membrane was measured at the midpoint between these two edges.
The PSD was manually traced using ImageJ, and the length was measured using the segmented line tool.
The synaptic vesicle area and distance to the nearest vesicle were quantified using a convolutional neural networks (CNNs) algorithm, as previously mentioned (Imbrosci et al., 2022).


Use of this data must reference Laura A. Volpicelli-Daley, Jacob E. Reiber, Dreson L. Russell, Saroj Sah, and Thomas Biederer.

Funding Information:

This research was funded in whole or in part by Aligning Science Across Parkinson’s to LV-D and TB (ASAP‐020616) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF).
