napari-molecular-cartography-viewer 0.1.1

A simple plugin to use Molecular Cartography Viewer within napari

napari-molecular-cartography-viewer

A napari dock widget to visualize exported molecular coordinate tables (CSV) as transcript points. It supports multi-gene overlay, value thresholding, and an optional gray background layer showing all transcripts.

This plugin is intended for exported/parsed coordinate tables (CSV). It does not require or reverse-engineer any proprietary file formats.

Compatibility

• Python: 3.10–3.13 (tested on 3.11)
• napari: 0.6.x (tested on 0.6.6)

CSV format requirements

The plugin auto-detects 4 required fields. Column names may vary, but must match one of the accepted names below.

Required columns

Field	Meaning	Accepted column names
x	X coordinate (pixel)	x, X
y	Y coordinate (pixel)	y, Y
gene	Gene / target name	gene, Gene, target, ID
val	Numeric value (intensity/score/confidence)	val, value, intensity, score, confidence, qc, V, v

Notes:

• napari points are rendered in (y, x) order internally.
• val must be numeric; non-numeric/NaN rows are automatically dropped.
• The CSV must contain a header row.

Minimal example

x,y,gene,val
120.5,88.2,GLYMA_01G000100,12.3
121.0,88.9,GLYMA_01G000100,8.1
500.2,410.7,NOD26,30.0

Usage

1. Start napari.
2. Open the viewer: Plugins → Molecular Cartography Viewer
3. Click Choose CSV… and select your exported/parsed .csv.
4. Search genes by substring, multi-select candidates, click Add →
5. Click Update display to render selected genes.

New in v0.1.1

• Added Apply UI Color button for active gene layers.
• Workflow for manual color changes in napari:
  1. Select a GENE: ... layer in the Layers panel (bottom-left).
  2. Change face color in layer controls (top-left).
  3. Click Apply UI Color in the plugin panel to apply the color to existing points.
• Added transcript/point count display for the active/selected layer (shown in the lower-right status area).
• Improved color update behavior for large transcript point layers.
• Improved background transcript layer handling to reduce unnecessary heavy loading in common use.

Options

• Show gray background layer: toggles All_transcripts
• Value threshold: keep points with val >= threshold (unless “Ignore threshold” is checked)
• Ignore threshold: show all points for selected genes
• Scale size by value: point size mapped to val
• Opacity / Base size: affects per-gene layers
• All point layers are forced to render with no borders for clean visualization.

Installation

From PyPI

pip install napari-molecular-cartography-viewer

If you need a full napari install in a fresh environment:

pip install "napari[all]" napari-molecular-cartography-viewer

Notes

Reading LZW-compressed TIFF images (optional)

If your background image is a TIFF with LZW compression, install imagecodecs:

conda install -c conda-forge imagecodecs

License

BSD-3-Clause. See LICENSE.