Evidence map›Paper›PMID 37577615›Full record

ArticlebioRxiv : the preprint server for biology2023

An end-to-end workflow for non-destructive 3D pathology.

Kevin W Bishop, Lindsey A Erion Barner, Qinghua Han, Elena Baraznenok, Lydia Lan, Chetan Poudel, Gan Gao, Robert B Serafin, Sarah S L Chow, Adam K Glaser and 8 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Kevin W BishopDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Lindsey A Erion BarnerDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Qinghua HanDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Elena BaraznenokDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Lydia LanDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Chetan PoudelDepartment of Chemistry, University of Washington, Seattle, Washington, USA.
Gan GaoDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Robert B SerafinDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Sarah S L ChowDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Adam K GlaserDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Andrew JanowczykDepartment of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.
David BrenesDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Hongyi HuangDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Dominie MiyasatoDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Lawrence D TrueDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
Soyoung KangDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.
Joshua C VaughanDepartment of Chemistry, University of Washington, Seattle, Washington, USA.
Jonathan T C LiuDepartment of Mechanical Engineering, University of Washington, Seattle, Washington, USA.

Funding

TRANSCRIPTOME AND PROTEOME STRATIFICATION OF PROSTATE ADENOCARCINOMA PHENOTYPESP50CA097186 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI PETER S NELSON · 2002 to 2026
$58.1M
KPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4M
NRSA Training CoreTL1TR002318 · NCATS · UNIVERSITY OF WASHINGTON · PI Megan Moore · 2017 to 2026
$8.4M
Resource Development CoreU54DK137328 · NIDDK · INDIANA UNIVERSITY INDIANAPOLIS · PI Pierre C Dagher · 2023 to 2026
$4.5M
Computational Pathology of Proteinuric DiseasesR01DK118431 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BARISONI, LAURA MARIACHIARA, HODGIN, JEFFREY BENTON · 2018 to 2025
$3.6M
Prostate cancer risk stratification via computational 3D pathologyR01CA268207 · NCI · UNIVERSITY OF WASHINGTON · PI Jonathan T.C. Liu, Anant Madabhushi · 2022 to 2026
$3.1M
Instrumentation platform for 3D pathology with open-top light-sheet microscopyR01EB031002 · NIBIB · UNIVERSITY OF WASHINGTON · PI LIU, JONATHAN T.C. · 2021 to 2024
$1.9M
Histotools: scaling digital pathology curation tools for quality control, annotation, labeling, and dataset identificationR01LM013864 · NLM · EMORY UNIVERSITY · PI JANOWCZYK, ANDREW ROBERT · 2022 to 2025
$1.4M
RadxTools for assessing tumor treatment response on imagingU01CA248226 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI TIWARI, PALLAVI, VISWANATH, SATISH EASWAR · 2020 to 2022
$1.4M
HistoTools: A suite of digital pathology tools for quality control, annotation and dataset identificationU01CA239055 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI JANOWCZYK, ANDREW ROBERT, MADABHUSHI, ANANT · 2019 to 2022
$1.0M
Light-sheet micro-aspiration microscopy for the isolation and analysis of rare tumor cells from intact clinical specimensR00CA240681 · NCI · ALLEN INSTITUTE · PI GLASER, ADAM K · 2021 to 2023
$745k
NCATS NIH HHS TL1 TR002318NCI NIH HHS P50 CA097186NCI NIH HHS R00 CA240681NCI NIH HHS R01 CA268207NCI NIH HHS U01 CA239055NCI NIH HHS U01 CA248226NIBIB NIH HHS R01 EB031002NIDDK NIH HHS R01 DK118431NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U54 DK137328NLM NIH HHS R01 LM013864
6 · The paper itself

Abstract

Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.

Identifiers

PMID37577615
PMCPMC10418226

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.