A collection is a software that encapsulate a set of bioimage components and/or workflows.

CellProfiler Analyst CPA

Description

CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

CPA

Mask-RCNN

Description

This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image. It's based on Feature Pyramid Network (FPN) and a ResNet101 backbone.

sumproduct

Description

An implementation of Belief Propagation for factor graphs, also known as the sum-product algorithm

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pydensecrf

Description

This is a (Cython-based) Python wrapper for Philipp Krähenbühl's Fully-Connected CRFs (version 2).

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PyTorch

Description

PyTorch is an open-source machine learning library for Python, based on Torch, used for applications such as natural language processing.

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pyBPDL

Description

The Binary Pattern Dictionary Learning (BPDL) package is suitable for image analysis on a set/sequence of images to determine an atlas of a compact region. In particular, the application can be maping gene activation accross many samples, brain activations in a time domain, etc.

Atlas