Confocal Microscopy Pancreatic Ducts Segmentation Dataset

This repository contains a dataset of several raw pancreas confocal microscopy four-dimensional (x, y, z, time) grey-scale image-stacks, each of them taken from an embryonic organ developing ex vivo over time. Each field of view contains only a part of one pancreas, and some images are therefore acquired from the same biological sample. The recorded signal corresponds to the tubular structure of the developing pancreatic duct. The apical domain of ductal cells was visualized by the red fluorescent protein mCherry, which was fused genetically to the protein MUCIN1. These raw images are provided here separated in 2D slices to facilitate processing. It also includes several smaller patches, extracted from the original images, and their corresponding binary manual annotations marking the pancreatic ducts in these images. These initially 3D patches are provided as well as separated 2D slices (both for the images and masks) to facilitate processing. Some simple python scripts are also included to be able to switch from these 2D arrangements to the original 3D versions of raw images and patches.