Back

Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish

Vohra, S. K.; Eberle, M.; Boulanger-Weill, J.; Petkova, M. D.; Schuhknecht, G. F. P.; Herrera, K. J.; Kämpf, F.; Ruetten, V. M. S.; Lichtman, J. W.; Engert, F.; Randlett, O.; Bahl, A.; Isoe, Y.; Hege, H.-C.; Baum, D.

2025-07-15 neuroscience
10.1101/2025.07.14.664689 bioRxiv
Show abstract

Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
Nature Methods
○ 385 papers in training set
Top 0.2%
23.0%
Similar papers in this journal
2
eLife
● 5828 papers in training set
Top 6%
13.3%
Similar papers in this journal
3
eneuro
● 439 papers in training set
Top 0.2%
10.1%
Similar papers in this journal
4
Development
● 497 papers in training set
Top 2%
5.0%
Similar papers in this journal
50% of probability mass above
5
Cell Reports Methods
○ 165 papers in training set
Top 0.3%
4.4%
Similar papers in this journal
6
Nature Communications
○ 5641 papers in training set
Top 31%
4.2%
7
Bioinformatics
◐ 1204 papers in training set
Top 5%
3.3%
8
PLOS Computational Biology
● 1863 papers in training set
Top 11%
2.7%
9
Neuron
○ 337 papers in training set
Top 3%
2.5%
10
Cell Reports
○ 1498 papers in training set
Top 18%
1.8%
11
Frontiers in Neuroinformatics
○ 41 papers in training set
Top 0.3%
1.8%
12
Communications Biology
○ 993 papers in training set
Top 17%
1.5%
13
iScience
○ 1154 papers in training set
Top 23%
1.4%
14
Nature
○ 645 papers in training set
Top 8%
1.4%
15
Neuroinformatics
○ 46 papers in training set
Top 0.6%
1.2%
16
PLOS Biology
● 486 papers in training set
Top 8%
1.1%
17
Biology Open
● 156 papers in training set
Top 3%
1.1%
18
Nature Neuroscience
○ 252 papers in training set
Top 4%
1.0%
19
GigaScience
◐ 212 papers in training set
Top 4%
1.0%
20
Life Science Alliance
● 285 papers in training set
Top 6%
1.0%
21
Scientific Reports
○ 3612 papers in training set
Top 71%
0.9%
22
Nature Protocols
○ 33 papers in training set
Top 0.5%
0.9%
23
Journal of Neuroscience Methods
○ 122 papers in training set
Top 2%
0.6%
24
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 43%
0.6%
25
Cell
○ 431 papers in training set
Top 11%
0.6%
26
Nature Computational Science
○ 55 papers in training set
Top 2%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.