Analysis Vignettes

• Example: Segmenting a Small Dataset Saved on a Local Hard Drive
  • Before Beginning: System Set Up
  • Step 1: Install vpt in a Virtual Environment
  • Step 2: Identify Cell Boundaries from Images (Cell Segmentation)
  • Step 2: Partition Transcripts into Cells
  • Step 3: Calculate Cell Metadata
  • Step 4: Update the .vzg File
• Example: Re-segmenting a MERSCOPE Heart Dataset with a Machine Learning Model Customized with Manual Annotations
  • Introduction
  • System Setup
  • Step 1: Evaluate Baseline Segmentation
  • Step 2: Identify Regions to Target for Segmentation Model Retraining and Extract Image Patches
  • Step3: Annotate Cell Boundaries on Extracted Image Patches
  • Step 4: Retrain the Machine Learning Model Using the Annotations
  • Step 5: Re-segment Full MERSCOPE Dataset Using Retrained Model
  • Step 6: Evaluate New Segmentation