Explore and filter flowcell data

Use the Flow Cell and Montage views to visualize, filter, and compare cells in a CytoCanvas Studio canvas.

The flow cell view

CytoCanvas Studio™ provides the Flow Cell view, which displays the full spatial layout of a flow cell. Navigate wells to inspect cell morphology, protein markers, and transcript locations. Use the panel controls to adjust channel visibility, cell boundaries, and metadata overlays. The Flow Cell view supports basic run QC, segmentation mask verification against raw fluorescence images, and spatial analysis of RNA transcripts and proteins.

Apply features to curate the cell images

Use the sidebar panel controls to adjust channel visibility, overlay boundaries, customize colors, and fine-tune your visualization in Flow Cell and Montage views.

Action	Panel	Description
View cell morphology and boundaries		View cell paint images and confirm cell and nuclear segmentation. Select or clear a channel checkbox to show or hide the target. Select the color to assign a custom color to a channel. Drag the contrast slider to set channel [begin, end] intensity range. Turn cell and nuclear boundaries on. Display well and tile labels.
View protein and transcript points		View spatially located cell features like RNA transcripts and proteins. Add RNA transcript and protein points by target name. Drag the Marker size slider to increase or decrease the size of marker dots. Toggle Show batch to display or hide batch name labels. Use the search bar to locate a specific protein or transcript. Select or clear a target checkbox to show or hide it. Select the target color to assign a custom color to a target.
Group cells by category		Select a non-numeric column from the Cell Table to use as the category source and color-code cells based on the categorical data. Toggle colored cell overlay on or off for the selected category. Drag the slider to set overlay transparency over other image layers. Use the category legend to toggle individual values on or off and assign custom colors.
Configure the flow cell view options		Adjust the viewport of the flowcell. Set the exact x and y location of the viewport. Show or hide the minimap. Show or hide the scale bar.

Create a saved flowcell view

A saved view is a snapshot of all visualization settings applied to a flowcell. Use saved views to bookmark specific visualization states and return to them later, or use the view switch to compare two flowcell views. Saved views capture the following selections:

• Selected channels, channel color, and channel contrast limits
• Cell and nuclear boundary display
• Viewport position, zoom level, and view settings
• Selected transcript and protein points
• Applied cell groups and categories settings

Save a view

1. Configure the visualization to the desired state.
2. From the top bar, select the Save dropdown.
3. Select Save as new view.
4. Enter a name and an optional description.
5. Select Save View.

   The view is saved and can be selected from the view dropdown.

Update an existing view

1. With a view selected, adjust the visualization settings as needed.
2. From the top bar, select the Save dropdown.
3. Select Save current.

   The selected view is overwritten with the current settings.

Export a flowcell or montage image

A flowcell or montage image can be exported.