CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler’s infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.

The Flickr30k dataset has become a standard benchmark for sentence-based image description. This paper presents Flickr30k Entities, which augments the 158k captions from Flickr30k with 244k coreference chains, linking mentions of the same entities across different captions for the same image, and associating them with 276k manually annotated bounding boxes. Such annotations are essential for continued progress in automatic image description and grounded language understanding. They enable us to define a new benchmark for localization of textual entity mentions in an image. We present a strong baseline for this task that combines an image-text embedding, detectors for common objects, a color classifier, and a bias towards selecting larger objects. While our baseline rivals in accuracy more complex state-of-the-art models, we show that its gains cannot be easily parlayed into improvements on such tasks as image-sentence retrieval, thus underlining the limitations of current methods and the need for further research.

This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images.

Donation after cardiac death liver transplantation is marred by inferior outcomes including higher rates of biliary complications and IC as well as increased mortality and graft failure. Despite current federal mandates to increase DCD donation, these serious complications translate into poor outcomes for individuals and increased healthcare costs. These risks should be considered in decisions regarding the utilization of these grafts.

We present an active detection model for localizing objects in scenes. The model is class-specific and allows an agent to focus attention on candidate regions for identifying the correct location of a target object. This agent learns to deform a bounding box using simple transformation actions, with the goal of determining the most specific location of target objects following top-down reasoning. The proposed localization agent is trained using deep reinforcement learning, and evaluated on the Pascal VOC 2007 dataset. We show that agents guided by the proposed model are able to localize a single instance of an object after analyzing only between 11 and 25 regions in an image, and obtain the best detection results among systems that do not use object proposals for object localization.