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α-Synuclein overexpression increases the tropism of pre-formed fibrils and MSA-patient derived seeds towards oligodendroglia.

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Paper

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The authors' code

Markdown · 40 lines · 1.7 KB · no license

  3. ## Pipeline
  5. Run the follwing script (to run on project, select `Run for project`)
  7. - export_annotation_script
  8. - Parameters: No parameters to modify
  9. - Output: Annotations (region and manually annotated pSyn) will be saved to folder with suffix (.geojson)
  11. - aspect_ratio_w_circularity
  12. - Parameters:
  13. - threshlod_level: threshold level for the green/2nd/pSyn Channel
  14. - red_threshold: threshold level for the red/1st Channel
  15. - gauss: Gauss filtering of the pSyn channel before masking (in number of pixels)
  16. - circularity_low: circularity level, 0 means not used
  17. - maxAspectRatio: maximum aspect ratio (long axis/short axis)
  18. - size_low = 15: minimum size to remove too small objects
  20. - Output: original image with a fourth channel based on the second channel where too elongated and too small objects will be removed, while annoations will be lost
  22. **Make sure to load the new images to the project and move them to Selected by clicking the `>>` arrow (see attached image)**
  24. - import_annoation_script
  25. - Parameters: No parameters to modify
  26. - Output: image with a fourth channel from previous step and with annoations loaded
  28. - cell_detection
  29. - Parameters: No parameters to modify
  30. - Output: image with a fourth channel from previous step and with annoations loaded
  31. - Note: need to make sure that the region annoation is before the pSyn annotation
  32. - run_object_classifier
  33. - Parameters: `classifier name`: the classifier created
  34. - Output: image with a fourth channel from previous step and with annoations loaded
  35. - Note: need to make sure that the region annoation is before the pSyn annotation
  37. Classify -> Object classification -> Create single measurement classifier
  40. ![b](batch.png)

README.md at commit 2700b64, no license · at the source

Overview

Authors: Anne-Line Strange Laursen1,2,3,4, Frida Lind-Holm Mogensen1,2, Jonas Folke1,2, Marie Frederikke Garnæs1,5, Luisa Harriet Knecht1,2, Tomasz Brudek1,2, Mikkel Vestergaard Olesen1,2, Marlene Bidstrup1, Sanne S. Kaalund1,5, Susanne Holst-Williams1,2, Katarina Willén4, Michelle Pinho6, Sandra Pritzkow6, Alexander K. Buell7, Azad Farzadfard7, Claudio Soto6, Karina Fog4, Louise Torp Dalgaard3, Florence Sotty4, Susana Aznar1,2
ORCID iDs: Frida Lind-Holm Mogensen, Luisa Harriet Knecht, Alexander K. Buell, Azad Farzadfard, Louise Torp Dalgaard, Susana Aznar
  1. Centre for Neuroscience and Stereology, Department of Neurology, Copenhagen University Hospital, Bispebjerg and Frederiksberg Hospital,Nielsine Nielsens Vej 6B, Entrance 11B, 2. Floor, DK-2400 Copenhagen, NV Denmark
  2. Copenhagen Center for Translational Research, Copenhagen University Hospital, Bispebjerg and Frederiksberg Hospital,Nielsine Nielsens Vej 4B, Entrance 80, DK-2400 Copenhagen, NV Denmark
  3. Department of Science and Environment, Roskilde University,Universitetsvej 1, DK-4000 Roskilde, Denmark
  4. H. Lundbeck A/S,Ottiliavej 9, DK-2500 Valby, Denmark
  5. Department of Health Technology, Technical University of Denmark,Ørsted Plads 349, 1, DK-2800 Kgs. Lyngby, Denmark
  6. Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School,Houston, TX USA
  7. Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark,Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
Institutions: Copenhagen University Hospital (Denmark); Roskilde University (Denmark); Lundbeck (Denmark) (Denmark); Technical University of Denmark (Denmark); The University of Texas Health Science Center at Houston (United States)
Journal: Acta neuropathologica communications, volume 14, issue 1, article 172
Dates: received 4 February 2026; accepted 5 June 2026; published online 13 June 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s40478-026-02346-3 · PMID 42288827 · PMCID PMC13491732 · OpenAlex W7164655754
Open access: gold, a free copy (OpenAlex)
Status: empty repository
Categories: human (organism), mouse (organism), Parkinson's (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Connectivity, fMRI & imaging
Keywords: Alpha-synuclein, MSA, PD, Synuclein mouse model, Human-derived fibrils, Oligodendroglia, Seed amplification assay
MeSH: alpha-Synuclein*, Brain*, Multiple System Atrophy*, Oligodendroglia*, Animals, Disease Models, Animal, Female, Humans, Inclusion Bodies, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Myelin Basic Protein (* major topic)
Topic: Parkinson's Disease Mechanisms and Treatments (Neurology, Medicine), according to OpenAlex
Funding: Copenhagen University
Citations: cited by 1 paper (Europe PMC); 59 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above.

DBI-INFRA/pSynDetectQuPath

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 2700b6423497d143bfb8546d1b750d283fcac642, 4 December 2024
Size: 7 files, 0 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
1 file
At the source: github.com/DBI-INFRA/pSynDetectQuPath

The paper's code and data availability statement is in the Data section.

Tracing map

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What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

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Read it in the paper: doi.org/10.1186/s40478-026-02346-3.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 20 authors, 7 keywords, 14 MeSH terms, 1 funder, 58 references.

Cite

This paper

Laursen, A.-L. S., Lind-Holm Mogensen, F., Folke, J., Garnæs, M. F., Knecht, L. H., Brudek, T., Olesen, M. V., Bidstrup, M., Kaalund, S. S., Holst-Williams, S., Willén, K., Pinho, M., Pritzkow, S., Buell, A. K., Farzadfard, A., Soto, C., Fog, K., Dalgaard, L. T., Sotty, F., & Aznar, S. (2026). α-Synuclein overexpression increases the tropism of pre-formed fibrils and MSA-patient derived seeds towards oligodendroglia. Acta neuropathologica communications, 14(1), 172. https://doi.org/10.1186/s40478-026-02346-3

BibTeX

@article{laursen2026synuclein,
author = {Laursen, Anne-Line Strange and Lind-Holm Mogensen, Frida and Folke, Jonas and Garnæs, Marie Frederikke and Knecht, Luisa Harriet and Brudek, Tomasz and Olesen, Mikkel Vestergaard and Bidstrup, Marlene and Kaalund, Sanne S. and Holst-Williams, Susanne and Willén, Katarina and Pinho, Michelle and Pritzkow, Sandra and Buell, Alexander K. and Farzadfard, Azad and Soto, Claudio and Fog, Karina and Dalgaard, Louise Torp and Sotty, Florence and Aznar, Susana},
title = {{α-Synuclein overexpression increases the tropism of pre-formed fibrils and MSA-patient derived seeds towards oligodendroglia}},
journal = {Acta neuropathologica communications},
year = {2026},
month = jun,
volume = {14},
number = {1},
pages = {172},
publisher = {BMC},
issn = {2051-5960},
doi = {10.1186/s40478-026-02346-3},
url = {https://doi.org/10.1186/s40478-026-02346-3},
pmid = {42288827},
pmcid = {PMC13491732}
}

RIS

TY - JOUR
AU - Laursen, Anne-Line Strange
AU - Lind-Holm Mogensen, Frida
AU - Folke, Jonas
AU - Garnæs, Marie Frederikke
AU - Knecht, Luisa Harriet
AU - Brudek, Tomasz
AU - Olesen, Mikkel Vestergaard
AU - Bidstrup, Marlene
AU - Kaalund, Sanne S.
AU - Holst-Williams, Susanne
AU - Willén, Katarina
AU - Pinho, Michelle
AU - Pritzkow, Sandra
AU - Buell, Alexander K.
AU - Farzadfard, Azad
AU - Soto, Claudio
AU - Fog, Karina
AU - Dalgaard, Louise Torp
AU - Sotty, Florence
AU - Aznar, Susana
TI - α-Synuclein overexpression increases the tropism of pre-formed fibrils and MSA-patient derived seeds towards oligodendroglia
T2 - Acta neuropathologica communications
J2 - Acta Neuropathol Commun
PY - 2026
DA - 2026/06/13
VL - 14
IS - 1
SP - 172
SN - 2051-5960
PB - BMC
DO - 10.1186/s40478-026-02346-3
UR - https://doi.org/10.1186/s40478-026-02346-3
LA - en
ER -

CSL-JSON

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