Cluster Map

Gene 1: None selected
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Gene 2: None selected
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Paste your gene list to check with the "Last gene" and "Next gene" buttons.

Expression Heatmap

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Here are the imputed gene expression for cells in single-molecule fluorescence in situ hybridization (smFISH) for maize ear at stage shown in the image using 60 genes for similarity analysis with the scRNA-seq data based on the methods decribed in Xu et al. 2025 and Demesa-Arevalo et al. 2025. Please check the reference below for details of the smFISH experiment and gene imputation process. W2.5 stage alone has 70878 imputed genes, W3.5 stage alone has 72475 imputed genes, and the merged data set has 74464 imputed genes. Below is just a quick guide:

  1. On the left panel (Cluster Map), you can view all or a few clusters of the smFISH with 60 genes.
  2. On the right panel (Expression Heatmap), you can check single gene or a pair of gene expression in each cell of the 4 smFISH images.
  3. "Gene 1" has heatmap for the cell fill color; "Gene 2" has heatmap for the cell border color. Values are counts per million per cell
  4. Select "Gene 1" or "Gene 2" will clear the cluster colors; and "Gene 1" compete the color fill colors with clusters.
  5. Gene 2 and the clusters can be shown at the same time, but make sure to select "Gene 2" first, then select the clusters.
  6. The imputed gene expression has background noises and you can filter the minimum counts to get cleaner heatmap. The default threshold is 25th percentile.
  7. You can use the mouse wheel to zoom in or out; drag it to move.Click reset if need to fully zoom out.
  8. You can also select cells in a region and get all its imputed transcripts by clicking "Enable Cell Selection" button.
  9. You can download a SVG (Scalable Vector Graphics) format image or a high-quality PNG image.
  10. You can now click "Enable Cell Selection" to select a group of cells and export all the imputed transcripts of these cells.
  11. You can now check a list of genes quickly by pasting them into the textbox on the bottom left corner; then go to top right corners and use the "Last Gene" and "Next Gene" button to check.

Reference

Xu X et al.,. Integration and imputation of single-cell and spatial transcriptomics uncover meristem dynamics in maize ear inflorescence. unpublished. 2026 . Please email both Drs. Xiaosa Xu (xjkxu@ucdavis.edu) and David Jackson (jacksond@cshl.edu) before using the data for your research and publication.