Evidence map›Paper›PMID 38948743›Full record

ArticlebioRxiv : the preprint server for biology2025

VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles.

Yasmin M Kassim, David B Rosenberg, Samprita Das, Zhuoling Huang, Samia Rahman, Ibraheem Al Shammaa, Samer Salim, Kevin Huang, Alma Renero, Cayla Miller and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

14 authors.

Yasmin M KassimDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.ORCID 0000-0001-5339-8081
David B RosenbergDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.
Samprita DasDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.ORCID 0009-0009-4321-0677
Zhuoling HuangDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.
Samia RahmanDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.
Ibraheem Al ShammaaDept. of Cellular and Molecular Biology, University of California, Berkeley, CA, 94720.
Samer SalimDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.
Kevin HuangDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.
Alma ReneroDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.ORCID 0009-0006-7874-7958
Cayla MillerDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.ORCID 0000-0001-8382-0255
Yuzuru NinoyuDept. of Otolaryngology, University of California, San Diego, La Jolla, CA, 92093.ORCID 0000-0002-9407-4697
Rick A FriedmanDept. of Otolaryngology, University of California, San Diego, La Jolla, CA, 92093.ORCID 0000-0002-5490-8562
Artur IndzhykulianDept. of Otolaryngology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA, 02115.ORCID 0000-0002-2076-6818
Uri ManorDept. of Cell & Developmental Biology, University of California San Diego, La Jolla, CA, 92093.ORCID 0000-0002-9802-1955

Funding

San Diego Nathan Shock CenterP30AG068635 · NIA · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI SHADEL, GERALD · 2020 to 2024
$6.0M
Molecular Basis of Hair Cell Stereocilia Bundle MorphologyR01DC017166 · NIDCD · MASSACHUSETTS EYE AND EAR INFIRMARY · PI INDZHYKULIAN, ARTUR · 2018 to 2022
$3.5M
Development of Gene Therapy for Hereditary Deafness using Rational Protein EngineeringR01DC020190 · NIDCD · MASSACHUSETTS EYE AND EAR INFIRMARY · PI DAVID P COREY, Artur Indzhykulian · 2022 to 2026
$3.3M
Investigating the mechanisms of stereocilia length regulation and innovative strategies for restoring hearingR01DC021075 · NIDCD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Uri Manor · 2023 to 2026
$3.2M
NIA NIH HHS P30 AG068635NIDCD NIH HHS R01 DC017166NIDCD NIH HHS R01 DC020190NIDCD NIH HHS R01 DC021075
6 · The paper itself

Abstract

Cochlear hair cells are essential for hearing, and their stereocilia bundles are critical for mechanotransduction. However, analyzing the 3D morphology of these bundles can be challenging due to their complex organization and the presence of other cellular structures in the tissue. To address this, we developed VASCilia (Vision Analysis StereoCilia), a Napari plugin suite that automates the analysis of 3D confocal microscopy datasets of phalloidin-stained cochlear hair cell bundles. VASCilia includes five deep learning-based models that streamline the analysis process, including: (1) Z-Focus Tracker (ZFT) for selecting relevant slices in a 3D image stack; (2) PCPAlignNet (Planar Cell Polarity Alignment Network) for automated orientation of image stacks; (3) a segmentation model for identifying and delineating stereocilia bundles; (4) a tonotopic Position Prediction tool; and (5) a classification tool for identifying hair cell subtypes. In addition, VASCilia provides automated computational tools and measurement capabilities. Using VASCilia, we demonstrate its utility on challenging datasets, including neonatal wildtype and

Identifiers

PMID38948743
PMCPMC11212889

What Socratic holds

Textmetadata
LicenceCC BY
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 Socratic graph.