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Image Analysis

The Cell Observatory provides access to various image analysis tools and workflows. This section covers different software packages and approaches for analyzing microscopy data.

Available Tools

  • CellPose - Deep learning-based cell segmentation
  • CellProfiler - Pipeline-based image analysis
  • Fiji - ImageJ-based analysis platform
  • Ilastik - Interactive machine learning for image analysis
  • Micro-SAM - Segment Anything Model for microscopy
  • TrackMate - Object tracking in Fiji

Environment Setup

For Python-based tools, see our guide on setting up your Conda environment.

Version Control

Learn about using GitHub for managing your analysis scripts and workflows.