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Introduction
Notebooks and Napari Widgets for Deep Learning
Tools used for this workshop
Setup
Pixi
Dependencies
Code and Data
Suggested exercises
Labeling and Augmentation
Some Napari Basics
File Organization
Explore and label data
Augmentation
Make patches from labels
Stardist training example
Train a cellpose 2D model
Sparse Labeling
Explore and label the ‘sparse labels’ Data
Make patches from labels
Sparse Stardist training example
Scale
Stardist compute receptive field
Cellpose trained to learn scale
Label and Predict
Make patches from labels
Train a cellpose 2D model for different scales
Large objects with protrusions and “self prediction”
Segment Everything with SAM
Explore data with SAM
Viewing and exploring overlapping labels
Filtering Labels
2025 Updates and Advances
Setup
Pixi
Test Pixi Environment
Microsam via Pixi environment example
Cellposesam (cellpose 4) via Pixi
Appose
Simple Appose Test
Run Cellpose with appose
Run multiple frameworks with Appose
napari-easy-augment-batch-dl
Easy-Augment-Batch-DL with Cell Data
Finetuning Segment Anything with
µsam
Easy-Augment-Batch-DL with Vessel Data
Repository
Open issue
Index
