W3.5 Cluster Map


Gene 1: None selected
Display threshold:
Gene 2: None selected
Display threshold:




Paste your gene list to check with the "Last gene" and "Next gene" buttons.

Expression Heatmap

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To make it easier to view, I downloaded barley spatial and scRNA-seq data from BARVISTA. Here are the imputed gene expression for cells in single-molecule fluorescence in situ hybridization (smFISH) for barley apex at 2 stages (late double ridge (W0.5, vegetative shoot apical meristem (vSAM)) and floret primordia (W3.5) stages; W3.5 has two vertical images and a transverse section) using 100 genes for similarity analysis with the scRNA-seq data. Please check the reference below for details of the smFISH experiment and gene imputation process. You can find the best hit of wheat genes on Arabidopsis, rice, and barley here: https://junli.netlify.app/apps/wheat-homeolog/

Below is just a quick guide:

  1. On the left panel (W3.5 Cluster Map), you can view all or a few clusters of the smFISH genes for W3.5 vertical images.
  2. On the right panel (Expression Heatmap), you can check single gene or a pair of gene expression in each cell.
  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 10% of maximum.
  7. You can use the mouse wheel to zoom in or out; drag it to move.
  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 pasating them in to the textbox on the bottom left corner; then go to top right corners and use the "Last Gene" and "Next Gene" button to check.
  12. You can download barley gene IDs (Morex V3) of the 100 smFISH genes.

Reference

Demesa-Arevalo, E., Dӧrpholz, H., Vardanega, I. et al. Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development. Nat. Plants (2026). https://doi.org/10.1038/s41477-025-02176-6