Model-based segmentation

ToDo: add a few more but not too many specialised concepts under here.

Description

SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.

Description

Machine Learning made easy

APEER ML provides an easy way to train your own machine learning
models and segment your microscopy images. No expertise or coding required.

APEER

Description

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

Stardist
Description

ZEN and APEER – Open Ecosystem for integrated Machine-Learning Workflows

Open ecosystem for integrated machine-learning workflows to train and use machine-learning models for image processing and image analysis inside the ZEN software or on the APEER cloud-based platform

Highlights ZEN

  • Simple User Interface for Labeling and Training
  • Engineered Features Sets and Deep Feature Extraction + Random Forrest for Semantic Segmentation
  • Object Classification workflows
  • Probability Thresholds and Conditional Random Fields
  • Import your own trained models as *.czann files (see: czmodel · PyPI)
  • Import "AIModel Containes" from arivis AI for advanced Instance Segmentation
  • Integration into ZEN Measurement Framework
  • Support for Multi-dimensional Datasets and Tile Images
  • open and standardized format to store trained models
ZEN Intellesis Segmentation

ZEN Intellesis Segmentation - Training UI

ZEN Intellesis - Pretrained Networks

ZEN Intellesis Segmentation - Use Deep Neural Networks

Intellesis Object Classification

ZEN Object Classification

Highlights Aarivis AI

  • Web-based tool to label datasets to train Deep Neural Networks
  • Fully automated hyper-parameter tuning
  • Export of trained models for semantic segmentation and AIModelContainer for Instance Segmentation
Annotation Tool

APEER Annotation Tool