-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathidr0155-study.txt
102 lines (88 loc) · 8.74 KB
/
idr0155-study.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
# FILL IN AS MUCH INFORMATION AS YOU CAN. HINTS HAVE BEEN PUT IN SOME FIELDS AFTER THE HASH # SYMBOL. REPLACE THE HINT WITH TEXT WHERE APPROPRIATE.
# STUDY DESCRIPTION SECTION
# Section with generic information about the study including title, description, publication details (if applicable) and contact details
Comment[IDR Study Accession] idr0155
Study Title A new method for reliably detecting single fluorescent puncta in structured backgrounds
Study Type protein localization
Study Type Term Source REF EFO
Study Type Term Accession GO_0008104
Study Description Super-resolution and single-molecule microscopy are increasingly being applied to complex biological systems. While this can lead greater insight, it also means data analysis becomes more complex: fluorescent puncta must reliably and efficiently be detected in the low signal, high noise, heterogeneous background environments of cells and tissue. We present a bioimaging-segmentation method that accomplishes this. It detects features over a broad range of spatial scales: from single proteins to complex cell phenotypes. Our method outperforms the state-of-the-art in both precision and speed, using image gradients to separate Gaussian-shaped objects from background features. We demonstrate that this approach both works robustly on simple test systems, and that it enables us to extract previously unseen correlations between Parkinson’s Disease-relevant $\alpha$-synuclein oligomers and multiple different cells types in the human brain. This sensitive, computationally efficient approach will enable fluorescent puncta and cellular features to be distinguished in cellular and tissue environments with a sensitivity down to the level of the single protein.
Study Key Words Imaging Alpha-Synuclein Methods
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL
Study BioImage Archive Accession
Study Public Release Date 2024-03-05
# Study Publication
Study PubMed ID
Study Publication Title RASP: Optimal single puncta detection in complex cellular backgrounds
Study Author List Fu B, Brock E, Andrews R, Breiter J, Tian R, Toomey C, Lachica J, Lashley T, Ryten M, Wood N, Vendruscolo M, Gandhi S, Weiss LE, Beckwith JS, Lee SF
Study PMC ID
Study DOI
# Study Contacts
Study Person Last Name Fu Lee
Study Person First Name Bin Steven
Study Person Email bf341@cam.ac.uk sl591@cam.ac.uk
Study Person Address Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
Study Person ORCID 0000-0002-8816-2906 0000-0003-4492-5139
Study Person Roles First Author Principal Investigator
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Fu at al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000195
Term Source Name NCBITaxon EFO CMPO FBbi
Term Source URI http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/
# EXPERIMENT SECTION
# Experiment Section containing all information relative to each experiment in the study including materials used, protocols names and description, phenotype names and description. For multiple experiments this section should be repeated. Copy and paste the whole section below and fill out for the next experiment
Experiment Number 1
Comment[IDR Experiment Name] idr0155-fu-alphasynuclein/experimentA
Experiment Sample Type tissue
Experiment Description We took 5400 field of views from three Parkinson's disease (PD) cases in the anterior cingulate gyrus for microglia and neuron markers respectively, covering dimensions of 4mm x 4mm x 13µm per patient. Cells were stained in 488nm channel while alpha-synuclein protein was labelled in 561nm channel. The colocalization study was performed based on the locations of detected cells and alpha-synucleins.
Experiment Size 5D Images: 5400 Average Image Dimension (XYZCT): XYZC Total Tb: 0.72Tb
Experiment Example Images
Experiment Imaging Method spinning disk confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000253
Experiment Organism
Experiment Organism Term Source REF NCBITaxon
Experiment Organism Term Accession
Experiment Comments
# assay files
Experiment Assay File idr0155-experimentA-annotation
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO
Protocol Type Term Accession EFO_0003969
Protocol Description Tissue sections were incubated with primary antibodies; anti-phosphorated alpha-synuclein (ab184674, 1:500; ab59264, 1:200) ; Microtubule-Associated Protein 2 (ab254143, 1:500); ionized calcium-binding adapter molecule 1 (Wako – 019-19741, 1:1000) for 1h at room temperature. The sections were then washed three times for five minutes in PBS followed by the corresponding AlexaFluor secondary antibodies (anti-mouse 568, anti-rabbit 568, anti-mouse 488, anti-rabbit 488 all at 1:200) for an additional hour at room temperature in the dark. Sections were then washed three times for five minutes again in PBS and incubated in Sudan Black (0.1% for 10 minutes). Removal of Sudan Black occurred with three washes in 30% ethanol. Images were taken on a spinning disk confocal microscope (3i intelligent imaging) with a 200mW, 488nm laser (LuxX) and a 150mW, 561nm laser (OBIS). The objective lens was a Zeiss oil immersion objective (Alpha Plan-Apochromat 100x/1.46\,NA Oil TIRF Objective, M27). The microscope was controlled using a PC (Dell-Acquisition Workstation 310R) and SlideBook software produced by the manufacturer (3i intelligent imaging). two sCMOS cameras (Prime 95B, Teledyne Photometrics) was used for the image acquistion in two colour channels seperately (488nm for cells and 561nm for alpha-synuclein aggregates). The analysis software was a self-written code that was designed for feature detection over structured backgrounds. We analyzed the number of diffraction-limited alpha-synuclein per FoV, sum intensit per diffraction-limited alpha-synuclein per FoV and also their relationship to the cell position.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
Phenotype Term Name
Phenotype Term Accession
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Format
Feature Level Data File Description
Feature Level Data Column Name
Feature Level Data Column Description
# Processed Data Files
Processed Data File Name idr0155-experimentA-processed
Processed Data File Format tab-delimited text
Processed Data File Description This file contains information summarizing the averaged number of diffraction-limited alpha-synuclein per patient, the averaged sum intensity per diffraction-limited alpha-synuclein per patient, and the averaged colocalization likelihood between cell and diffraction-limited alpha-synuclein per patient
Processed Data Column Name Experimental Condition [Antibody1]_Experimental Condition [Antibody2] Experimental Condition [patientID] NumberOfImages NumberOfSpots IntensityOfSpots ColocalizationLikelihoodToCell
Processed Data Column Type experimental condition experimental condition data data data data
Processed Data Column Annotation Level experimental condition experimental condition image protein protein protein
Processed Data Column Description The antibody used for labelling the cell and labelling the alpha-synuclein which patient the data comes from number of images taken per patient Averaged number of diffraction-limited alpha-synuclein detected for each patient Averaged sum intensity for each diffraction-limited alpha-synuclein for each patient likelihood to be inside the cell (1 means no correlation, <1 means not likely to be found within cell, >1 means likely to be found within cell)
Processed Data Column Link To Assay File Experimental Condition [Antibody1]_Experimental Condition [Antibody2]