General Infromation
This dataset involves analysis of mice one month after injection of alpha-synuclein pre-formed fibrils or alpha-synuclein monomers.
Brain sections were taken from brgema +0.2mm and stained with antibodies against PSD-95,Synapsin, at pSynuclein S129.
Analysis of synaptic localization of pSYN, synaptic density, and association of synaptic pSYN to pSYN positive neurites was quantified.

File Overview
Files have been named by the endoints contained within each file.
All files are in a comma separated format.
All files are different analyses from the same imaging dataset.

Data Specific Information
Files:
Figure1D_pSYN_by_group.csv
	-This file contains the intensity of eiher synaptic pSYN or extrasynaptic pSYN on an imagewise basis
	-Column headings:
		-Mouse_ID : This is the animal ID. 
		-pSYN_intensity: This is the measured intensity of pSYN.
		-treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
		-field_type: This indicates if the data represents synaptic or extrasynaptic measurements.
		

Figure1I_mesoscan_pSYN_by_group.csv
	-This file contains the intensity synaptic pSYN on an imagewise basis.
	-Column headings:
		-Mouse_ID : This is the animal ID. 
		-synaptic_density: This is the measured synaptic density in um^3.
		-pSYN_intensity: This is the measured intensity of synaptic pSYN.
		-treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
		
FIgure2D_synaptic_pSYN_intensity_by_neurite_distance.csv
	This file contains the intensity synaptic pSYN as a function of distance to labeled pSYN positive neurites
	-Column headings:
		-Mouse_ID : This is the animal ID.
		-pSYN_aggregate_distance_to_synapse: This is distance a given synaptic loci is in microns from a pSYN positive neurite.
		-synaptic_pSYN_intensity: This is the measured intensity of synaptic pSYN.
		-treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
			-Only pff treated animals were analyzed since neurites could not be masked in monomer treated animals.
			
Figure2C_synaptic_density_by_neurite_intensity.csv
	This file contains the density of synaptic loci per voxel as a function of pSYN intiensity in masked neurites.
	-Column headings:
		-Mouse_ID : This is the animal ID. 
		-pSYN_aggregate_bin_intensirty: Neurite pSYN intensity.	
		-synaptic_density: Synaptic density within 800um of pSYN positive neurite.
		-treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
			-Only pff treated animals were analyzed since neurites could not be masked in monomer treated animals.

Figure3D_subtype_counts.csv
	This file contains counts of pSYN aggregates on an imagewise basis that have been identified as colocalized with axons or dendrites ipsilateral to the injection.
	-Columnn headings:
		counts_per_field: number of axon or dendrite type per field
		mouse_ID:This is the animal ID. 
		subtype: whether axon or dendrite
		field: image field

Figure3E_subtype_percents_by_aggregate_size.csv			
	This file contains counts of pSYN aggregates on an imagewise basis that have been identified as colocalized with axons or dendrites and then binned based upon pSYN aggregate size.
	-Columnn headings:
		pSYN_aggregate_size_bin: pSYN aggregate size of bin
		percent_counts: percentage of aggregates within bin that are a given subtype
		mouse_ID:This is the animal ID. 
		subtype: whether axon or dendrite

Figure8B_synaptic_density.csv
	This file contains the synaptic density of the entire layer 2/3 and layer 5 region of the imaged mesoscan.
	-Columnn headings:
		synaptic_density: Synaptic density within region
		Mouse_ID:This is the animal ID. 
		treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
		layer: cortical layer


Figure8C_synaptic_density.csv
	This file contains the synaptic density of secondary motor cortex separated into layer 2/3 and layer 5 regions.
	-Columnn headings:
		synaptic_density: Synaptic density within region
		treatment_group: This is the designation for eithr pre-formed fibrils (pff) or monomer treatment groups.
		layer: cortical layer

Figure8E_cortical_column_synaptic_pSYN.csv
	This file contains the synaptic pSYN intensity within cortical columns.
	-Columnn headings:
		layer 2/3: Layer 2/3 of cortex
		layer 5: Layer 5 of cortex
		column_pair: indentified cortical column

Figure8F_cortical_column_synaptic_density.csv
	This file contains the synaptic density within cortical columns.
	-Columnn headings:
		layer 2/3: Layer 2/3 of cortex
		layer 5: Layer 5 of cortex
		column_pair: indentified cortical column

FigureSup8_6mpi_cortical_column_synaptic_density.csv
	This file contains the synaptic pSYN intensity within cortical columns at 6 months post-injection.
	-Columnn headings:
		layer 2/3: Layer 2/3 of cortex
		layer 5: Layer 5 of cortex
		column_pair: indentified cortical column

FigureSup_subtype_randomization.csv
	This file contains the axon versus dendrite analysis of the original images and versions which randomize the spatial relationshio to pSYN aggregates.
	-Columnn headings:
		percent_colocalized: percent of pSYN aggregates identified as axon or dendrite
		subtype: axon versus dendrite
		analysis_type: whether analysis was performed on the original versus randomized data

FigureSup3F_subtype_counts_contralateral
	This file contains counts of pSYN aggregates on an imagewise basis that have been identified as colocalized with axons or dendrites contralateral to the injection.
	-Columnn headings:
		counts_per_field: number of axon or dendrite type per field
		mouse_ID:This is the animal ID. 
		subtype: whether axon or dendrite
		field: image field

FigureSup2_puncta_size_by_neurite_distance
	This file contains the average measurement of PSD-95 and synapsin puncta, identifying the post-synaptic and pre-synaptic terminals respectively, by the distance to nearest pSYN labeled aggregate.
	-Columnn headings:
		puncta_size: average puncta size normalized to most distal distance interval
		distance_to_neurite: distance in microns to the nearest neurite
		mouse_ID: This is the animal ID.
		subtype: whether PSD-95 or synapsin puncta


	
Methodology
This data was collected using a Zeiss 980 Airyscan microscope with a 63x 1.4NA objective.
Images were Airyscan pre-processed in Zeiss Zen Blue with a strength setting of 4.0.
Airyscan processed images were analyzed using the SEQUIN_v15 analysis workflow.


Data Access and Sharing
Use of this data must reference Terrance Kummer, Andrew Sauerbeck, Saroj Sah, and Thomas Biederer.
Datasets should be licensed with a CC BY 4.0 or CC0 license. 
This data was supported with funding from:

“This research was funded in whole or in part by Aligning Science Across Parkinson’s [ASAP Grant #] through the Michael J. Fox Foundation for Parkinson’s Research (MJFF).”

