Evidence map›Paper›PMID 40902674›Full record

ArticleJournal of neuroscience methods2025

Optimizing tissue clearing methods for improved imaging of whole-mount retinas and optic nerves.

Aubin Mutschler, Volha V Malechka, Nikita Bagaev, Petr Baranov, Jonathan R Soucy

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of neuroscience methods, 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Aubin MutschlerThe Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, United States; Program of Neuroscience, Middlebury College, Middlebury, VT 05753, United States.
Volha V MalechkaThe Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, United States.
Nikita BagaevThe Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, United States.
Petr BaranovThe Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, United States.
Jonathan R SoucyThe Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA 02114, United States; Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, United States; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States. Electronic address: jonathan_soucy@meei.harvard.edu.

Funding

VISION RESEARCHP30EY003790 · NEI · SCHEPENS EYE RESEARCH INSTITUTE · PI Patricia Ann D'Amore · 1985 to 2026
$25.5M
Retinal Ganglion Cell Replacement in Clinically Relevant Models of Optic NeuropathyU24EY029893 · NEI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI BARANOV, PETR, REX, TONIA S · 2018 to 2022
$7.2M
Regulating cell-cell interactions to improve donor retinal ganglion cell integrationF32EY033211 · NEI · SCHEPENS EYE RESEARCH INSTITUTE · PI SOUCY, JONATHAN R · 2022 to 2024
$222k
Regulating host neural activity to improve retinal ganglion cell replacement therapiesK99EY036122 · NEI · SCHEPENS EYE RESEARCH INSTITUTE · PI SOUCY, JONATHAN R · 2025 to 2025
$133k
NEI NIH HHS F32 EY033211NEI NIH HHS K99 EY036122NEI NIH HHS L70 EY034355NEI NIH HHS P30 EY003790NEI NIH HHS U24 EY029893
6 · The paper itself

Abstract

backgroundGene and cell therapies hold promise for restoring vision in hereditary and advanced optic neuropathies. Accurate evaluation of these therapies requires advanced imaging methods that can visualize transplanted cells within intact retinal tissue. NEW

methodWe present a whole-mount tissue-clearing workflow optimized for the mouse retina and optic nerve to improve visualization of donor neuron integration following cell transplantation. Five clearing methods were evaluated, and a modified protocol, ScaleH, was developed by adding polyvinyl alcohol to ScaleS to improve fluorescence preservation.

resultsScaleS yielded the highest transparency (46 % increase) and immunohistochemical clarity (89 % increase) in the retina among the tested methods. ScaleH retained comparable clarity while significantly reducing fluorescence decay over time (32 % less decay). ScaleH was compatible with endogenous reporters and immunolabeling, enabling detailed imaging of transplanted human stem cell-derived retinal neurons in the retinal ganglion cell layer, as well as visualization of neurites, microglia, and cell nuclei in the optic nerve. COMPARISON WITH EXISTING

methodsCompared to other clearing protocols, ScaleH provided superior fluorescence retention and stability without compromising optical clarity. Its compatibility with both immunostaining and endogenous fluorescent proteins supports broad application in imaging.

conclusionsScaleH is a reliable and high-resolution clearing method for imaging whole-mount retinas and optic nerves. It facilitates robust assessment of donor cell integration in regenerative ophthalmology and may be broadly applicable in neurobiological research.

Indexed as

Optic NerveRetinaAnimalsHumansMiceMice, Inbred C57BLStem Cell TransplantationImmunofluorescence imagingNeuron transplantationOptic nerveRegenerative ophthalmologyRetinaRetinal ganglion cellsTissue clearing

Identifiers

PMID40902674
PMCPMC12462138

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Registered trials

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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.