Evidence map›Paper›PMID 41700733›Full record

ArticleeLife2026

Deep neural networks to register and annotate cells in moving and deforming nervous systems.

Adam A Atanas, Alicia Kun-Yang Lu, Brian Goodell, Jungsoo Kim, Saba N Baskoylu, Di Kang, Talya S Kramer, Eric Bueno, Flossie K Wan, Karen L Cunningham and 2 more

Abstract read
In one paragraph

Article in eLife, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Adam A AtanasPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Alicia Kun-Yang LuPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Brian GoodellPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Jungsoo KimPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Saba N BaskoyluPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Di KangPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Talya S KramerPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Eric BuenoPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Flossie K WanPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.
Karen L CunninghamPicower Institute for Learning and Memory, Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.
Brandon WeissbourdPicower Institute for Learning and Memory, Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.
Steven W FlavellPicower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.ORCID https://orcid.org/0000-0001-9464-1877

Funding

Neural Mechanisms that Underlie Flexible Sensory Control of Behavioral States in C. elegansR01DC020484 · NIDCD · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Steven Willem Flavell · 2023 to 2026
$1.5M
Brain-Wide Representations of Behavior During Aversive Internal States in C. ElegansR01NS131457 · NINDS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Steven Willem Flavell · 2023 to 2026
$1.5M
Dissecting the functional organization of the serotonergic system in C. elegansR01GM135413 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI FLAVELL, STEVEN WILLEM · 2020 to 2023
$1.2M
Mechanisms of Network-Scale Neural Regeneration in a New Neuroscience ModelR01NS141960 · NINDS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Brandon Weissbourd · 2025 to 2026
$795k
A New Animal Model to Examine Nervous System Function Development and RegenerationR00NS119749 · NINDS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI WEISSBOURD, BRANDON · 2023 to 2025
$710k
Alfred P. Sloan Foundation Research ScholarHoward Hughes Medical Institute Investigator AwardKlingenstein-Simons FellowshipLife Sciences Research Foundation FellowshipMcKnight Foundation Scholars AwardMIT School of Science Mathworks FellowshipNIDCD NIH HHS R01 DC020484NIGMS NIH HHS R01 GM135413NIH HHS DC020484NIH HHS GM135413NIH HHS NS119749NIH HHS NS131457NIH HHS NS141960NINDS NIH HHS R00 NS119749NINDS NIH HHS R01 NS131457NINDS NIH HHS R01 NS141960Searle Scholars Program AwardU.S. National Science Foundation 1845663
6 · The paper itself

Abstract

Aligning and annotating the heterogeneous cell types that make up complex cellular tissues remains a major challenge in the analysis of biomedical imaging data. Here, we present a series of deep neural networks that allow for automatic non-rigid registration and cell identification, developed in the context of freely moving and deforming invertebrate nervous systems. A semi-supervised learning approach was used to train a

Indexed as

Caenorhabditis elegansDeep LearningImage Processing, Computer-AssistedNervous SystemNeural Networks, ComputerNeuronsAnimalscalcium imagingC. eleganscell segmentationcell trackingcell type annotationcomputational biologyjellyfishneuron identificationneurosciencesystems biology

Identifiers

PMID41700733
PMCPMC12912725

What OpenQuestion holds

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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.