Hi everyone,
I’m developing vdFISH (virtual double fluorescence in situ hybridization), a browser-based app for exploring two-gene co-expression in mouse brain spatial transcriptomic data from the Allen Brain Cell Atlas.
I designed its appearance to resemble the double-label fluorescence in situ hybridization images familiar to wet-lab researchers. The idea is to make it easy to explore a simple question: “Where are these two genes expressed, and which cells express both?”
You can try it here: Open vdFISH
What you can do
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Choose from a selection of brain regions and coronal sections.
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Search for one or two genes and visualize their spatial expression in a FISH-like display: red and green for the individual genes, and yellow for double-positive cells.
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Adjust the expression threshold for each gene and inspect positive-cell counts, percentages, and Jaccard overlap.
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Use it directly in a browser on a smartphone or PC, without installing software or writing code.
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Try a short quiz: predict which gene pair has the strongest overlap, then see the spatial pattern and scores.
For a quick example, open Explore vdFISH → OT to view Drd2 and Penk in the olfactory tubercle.
The app uses the Allen Brain Cell Atlas MERFISH-C57BL6J-638850 imputed-expression dataset and reconstructed coordinates. The display is a computational visualization inspired by fluorescence microscopy; it is not an experimental FISH image. Co-expression results depend on the underlying expression estimates and the selected thresholds.
I hope this will be useful for quick exploration, generating ideas for follow-up experiments, and learning spatial gene-expression patterns. The app is intended for academic research and education.
I would welcome feedback from the community, particularly on the visualization, usability on phones, and additional brain regions or features you would find useful.
Many thanks to the Allen Institute for making these data available. Dataset links and the primary publication are provided within the app.
Sora Mitamura
University of Fukui