time-series

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.

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.

The Incucyte® Base Analysis Software provides a guided interface and purpose-built tools, which include the process of acquiring, viewing, analyzing and sharing images of living cells.

FluoGAN is a fluorescence image deconvolution software combining the knowledge of acquisition physical model with gan. It takes a fluctuating sequence of blurred, undersampled and noisy images of the sample of interest  fixed sample as input from wide field or confocal and returns a super resolved image.