On the right hand side of the screen, you will find the Visualizer Menu. The first panel you will see open is the Channels Panel .
Study or Experiment: Select which Study or Experiment to view images from.
Regions: A selection menu for all the regions acquired for the study or experiment. You can open up to 4 regions in the Visualizer at a time. When you open a new region, the channels that are selected in the active region will also be opened on the new region. You can also make it easier to find regions by using the “filter regions” option.
Apply channel changes to all regions?: This option allows you to either apply channel configuration changes to the active region or to all open regions simultaneously.
Include region in downstream analysis?: If the acquisition contains serious problems across multiple channels, uncheck this box to exclude the region from downstream analysis. This box is checked by default, and does not necessarily represent a QC evaluation by Enable Medicine scientists.
Biomarkers: For viewing biomarker channels. Click the + icon to select biomarker channels to view.
Cell Overlays: For viewing overlay channels, such as segmentation masks and cell annotations. Click the + icon to select overlays to view.
At the bottom of the channels panel, you’ll find the Other Actions button, which offers additional functions:
Auto-contrast All Biomarker Channels: resets all biomarker channels to their auto-threshold valuesDownload Images: downloads images of the currently open regionsDownload Biomarker Channels: downloads a CSV of all regions’ biomarker channels and their metadataSave All Open Channel Configurations: saves the configurations of all open channels, and sets the current visualizer state to open automatically when this study is loaded.Once biomarker channels are selected, a box will appear for each channel. Click on the box to expand its controls.
Color: Click on the color indicator on the leftmost side of the controls to select the color that you want the channel to display.Auto-contrast: Restore the max and min threshold to their default values.Save: Save the channel configuration (color, min. and max. thresholds)