Step 1: Load Data

Step 1: Load Data#

CellPick supports two main workflows for loading data:

Option A: Traditional Image + XML Workflow#

This workflow is ideal for users who have microscopy images and pre-computed shape annotations in XML format.

Add Image Channels#

  • Click “Add Channel” to load one or more microscopy images

  • Supported formats: TIFF (.tif, .tiff) and CZI (.czi)

  • If your file contains multiple channels, CellPick will load them all sequentially

  • For each channel, you’ll be prompted to: - Enter a name for the channel - Select a display color

Load Image Channels UI

Load Shapes#

  • Click “Load Shapes” to import pre-existing shape annotations

  • This opens two sequential file dialogs: 1. Select the XML file containing shape coordinates 2. Select the calibration/metadata file for alignment

Load Shapes Dialog

Option B: SpatialData Workflow#

This workflow is for users working with SpatialData (.zarr) stores, which can contain images, segmentation masks, shapes, and annotations in a unified format.

Loading SpatialData#

  • Click “Add Spatial Data” to load a .zarr store

  • CellPick will detect available elements: - Images: Multi-channel microscopy images - Labels: Segmentation masks (cell boundaries) - Shapes: Pre-computed polygon shapes - Tables: Annotation tables with cell labels

  • For multi-resolution images, you’ll be prompted to select a resolution level: - Higher resolution = more detail but slower loading - Lower resolution = faster loading, automatic upscaling on export

Note

SpatialData support requires the spatialdata package. See Installation for details.

For multi-resolution images, you’ll be prompted to select a resolution level:

SpatialData resolution selection dialog

Once loaded, all channels appear in the control panel with per-channel visibility and saturation controls:

SpatialData loaded with channel controls
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