Metadata management for high content screening in OMERO

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org

A condition for the overflow stability of second-order digital filters that is satisfied by all scaled state-space structures using saturation

A set of conditions is derived that ensures overflow stability of second-order digital filters for different classes of overflow arithmetics, involving only the elements of the state-transition matrix. The well-known arithmetic saturation, zeroing, and two's-complement lead to different stability conditions, the condition for saturation being the least restrictive. As a result, all properly scaled second-order state-space structures are zero-input overflow stable if saturation is used for overflow correction. Conditions are derived for stable second-order digital filters in a nonzero input situation by introducing a weaker form of stability of the forced response. The analysis is based on determining the set of Lyapunov functions for a general second-order state-transition matrix, given a certain overflow arithmeti

Controlled Rounding in Low Noise Digital Filter Structures

Several IIR digital filter structures are known which exhibit freedom of limit cycles with magnitude truncation (MT) as rounding mechanism. Other well-known structures provide low noise properties with respect to quantization. Often, nonlinear stability and quantization noise reduction are incompatible. Integrator-based structures, for example, which are common for narrowband lowpass filter applications, show an excellent low noise behaviour but they are not free from limit cycles. With controlled rounding (CR), the direction of quantization is made dependent on some suitably chosen control signal within the structure. Such a quantization mechanism has been shown to stabilize the direct form structure [1] and is easy to implement: simply subtract the control signal from the signal to be quantized, truncate the difference (MT), and subsequently add the control signal. The more difficult part is to find a suitable control signal. This contribution describes how controlled rounding can be..