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Icescopy is a desktop application for reviewing freezing-array image sequences, annotating droplets or wells, generating grayscale measurement time series, identifying freeze events, and combining image-derived results with external temperature data.
This wiki is the package documentation set for the repository. It is split into task-focused pages instead of one large manual page.
This wiki is written for:
- users running the desktop application
- researchers reviewing image-derived freeze results
- maintainers who need architecture context
- Installation and Setup
- Quick Start
- Annotation Workflow
- Image Editing
- Analysis and Results
- Temperature Import
- Sessions, Export, and Preferences
- Troubleshooting
Most sessions follow this order:
- Start a session and load images.
- Sort the image sequence if needed.
- Annotate cells or droplets.
- Assign samples if the experiment uses sample groups.
- Run analysis.
- Review the grayscale plot and results tables.
- Import temperature data if needed.
- Save the session.
- Export the results.
A .icescopy file is the saved working state of an analysis session.
It stores session metadata, application state, and results tables.
A cell is the annotated region of interest used for grayscale measurement and freeze detection. Cells have stable IDs and can also be grouped into samples.
A keyframe stores a known cell layout at a particular frame. Icescopy interpolates between keyframes to reduce repetitive manual edits.
Freeze count timeseries combines image-derived freeze counts with external temperature timeseries, including repeated cooling-warming cycles when supported by the imported format.