library

Algorithm and software created to extract animal trajectories from videos of a collection of animals up to 100 individuals. Idtrackerai uses two convolutional networks: one for animal identification and another to detect when animals touch or cross each other.

This workflow describes a deep-learning based pipeline for reliable single-organoid segmentation and tracking in 2D+t high-resolution brightfield microscopy of mouse mammary epithelial organoids. The pipeline involves a four-layer U-Net to infer semantic segmentation predictions, adaptive morphological filtering to establish candidate organoid instances, and a shape-similarity-constrained, instance-segmentation-correcting tracking step to associate the corresponding organoid instances in time.

It is particularly focused on automatically detecting an organoid located approximately in the center of the first frame and track all its subsequent instances in the remaining frames, emphasizing on accurate organoid boundary delineation. Furthermore, segmentation network was trained using plausible pix2pixHD-generated bioimage data. Syntheric image simulator code and data are also available here.

OrganoSeg is an open-source software that integrates segmentation, filtering, and analysis for breast-cancer spheroid and colon and colorectal-cancer organoid morphologies.

OrganoID is an image analysis platform that automatically recognizes, labels, and tracks single organoids, pixel-by-pixel, in brightfield and phase-contrast microscopy experiments. The platform was trained on images of pancreatic cancer organoids and validated on separate images of pancreatic, lung, colon, and adenoid cystic carcinoma organoids.

JIPipe is a visual programming language to realize code-free workflow building for ImageJ-based image analyses. GUI, graphical user interface. Currently, JIPipe unifies the functionality of over 1,000 ImageJ commands into a standardized interface, represented as nodes in the pipeline flow chart. The window-based data management implemented in ImageJ is replaced with a table-based model designed for batch processing. JIPipe is also available from within the ImageJ update service.