View Tab

The View tab provides visualization and exploration capabilities for protein expression data and multi-channel microscopy images. Researchers can layer multiple protein channels, adjust display properties per layer, and select regions for downstream analysis.

Interface Overview

The View tab consists of two main sections:

Layer Control Panel (left): Manage individual protein/image layers and their display properties.
Visualization Canvas (right): The combined image with interactive region selection tools.

Loading Data

Before adding visualization layers, load your processed data:

Open Image: Load the cell segmentation image output from the Extract tab (typically a StarDist PNG or TIFF mask).
Open Cell Data: Load the per-cell protein expression CSV or Excel file produced by Quantification.
Scale Down Factor: Reduce the image resolution for performance when working with very large images.
Click Apply to prepare the data for visualization.

Layer Management

Add Layer

The Add Layer button lets you select a protein channel from your loaded cell data and add it to the canvas as a new visualization layer. Each protein channel is displayed independently and can be manipulated without affecting others.

Add Other Image

Use this button to import an external image (PNG, JPG, TIFF) as an additional overlay layer. Useful for adding reference images, brightfield overlays, or annotations.

Layer Controls

Each layer has its own control panel:

Control	Description
Opacity	Slider (0–100%). Adjusts transparency so underlying layers remain visible.
Contrast	Dual-slider for minimum and maximum intensity thresholds. Values below the minimum appear black; values above the maximum are shown at full brightness. Narrow the range to reveal faint signals.
Tint Color	Opens a color picker. Apply a color tint to the grayscale channel data. Common choices: red, green, blue (primary), cyan, magenta, yellow (complementary), or custom.
Visibility	Toggle button to show or hide a layer without removing it. Useful for comparing expression patterns.
Visibility Threshold	Hides cells not within quantile range. Useful for sepearting high/low populations. Use auto contrast after adjust threshold to see clearer view of low populations.
Delete Layer	Permanently removes the layer from the stack.

Region Selection Tools

In the top-right corner of the canvas, selection tools let you define regions of interest that feed into the Analysis tab:

Rectangle Selection (shortcut: R)
Circle Selection (shortcut: C)
Polygon/Lasso Selection (shortcut: L)

Export

Export the current canvas view as an image file:

Export to PNG: Saves a flattened RGB rendering of all visible layers with current opacity, contrast, and tint settings applied.
Export to multi-channel TIFF: Saves each layer as a separate channel in a multi-channel TIFF file, preserving the full intensity range with applied contrast settings.

UMAP Launcher

The UMAP dimensionality reduction visualizer can be launched from the View tab. This opens the UMAP interface which projects the per-cell, multi-protein expression data into a 2D plot for cluster exploration. See the Analysis Tab page for full details on the UMAP visualization.

Usage Tips

Assign complementary colors to proteins that co-localize (e.g. red + cyan) so overlap appears as a distinct hue.
For faint signals, narrow the contrast range (move both sliders toward the signal peak) to make them more visible.
Toggle visibility on and off to compare channel-by-channel without rearranging layers.
Use Scale Down Factor for initial exploration on large images; switch to full resolution before exporting.