Image segmentation

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 - Pretrained Networks

Intellesis 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

Quantitative Criterion Acquisition Network (QCA Net) performs instance segmentation of 3D fluorescence microscopic images. QCA Net consists of Nuclear Segmentation Network (NSN) that learned nuclear segmentation task and Nuclear Detection Network (NDN) that learned nuclear identification task. QCA Net performs instance segmentation of the time-series 3D fluorescence microscopic images at each time point, and the quantitative criteria for mouse development are extracted from the acquired time-series segmentation image. The detailed information on this program is described in our manuscript posted on bioRxiv.

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

It implements the template matching function from the OpenCV library. The java interface of OpenCV was done through the javacv library. It is quite similar as the existing template matching plugin but runs much faster and users could choose among six matching methods: 

1.Squared difference

2.Normalized squared difference

3.Cross-correlation

4.Normalized cross-correlation

5.Correlation coefficient

6.Normalized correlation coefficient

The detailed algorithms could be found here.

The cvMatch_Template will search a specific object (image pattern) over an image of interest by the user-specified method.