The successful implementation of a licensed data management interface between a Sunquest® laboratory information system and an AB SCIEXTM mass spectrometer

Abstract

Background:Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX™ mass spectrometer to our Sunquest® LIS.Materials and Methods:We licensed software for the data management interface from the University of Pittsburgh, but extended this work as follows: The interface was designed so that it would accept a text file exported from the AB SCIEX™ × 5500 QTrap® mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest® via file transfer protocol.Results:The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst® software to the required Sunquest® import format. This required writing of a “pre-processor” by one of the authors which was easily integrated with the supplied software.Conclusions:We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.

A gamma-gaussian mixture model for detection of mitotic cells in breast cancer histopathology images

“…The set of textural features extracted from a window of size 30 × 30 pixels around the bounding box of each candidate mitosis are as follows: 32 Phase Gradient (PG) features (16 orientations, 2 scales),[7] 1 roughness feature, 1 entropy feature. From each of these 34 features, 4 representative features were computed: (1) mean, (2) standard deviation, (3) skewness, (4) kurtosis.…”

Computer-based image analysis in breast pathology

“…The studies are summarized in Table 1. In this section, methods proposed for segmenting DRAs,[31323334] epithelial nuclei,[5151617181935] lymphocyte cells,[71320] tubule,[2122232425] and mitotic figures[682627282930] are discussed.…”

“…Therefore, in a study by Mercan et al .,[32] a texton-based approach was proposed to distinguish between DRAs and irrelevant patches. In another study by Khan et al .,[31] Gabor-based texture features were used to differentiate hypocellular from hypercellular stroma. Gabor filters are extensively used in image analysis as they resemble the human visual system.…”

Clinical Microbiology Informatics

“…Unfortunately, interfacing each of these peripheral instruments with the LIS is not always pursued or is deemed too resource intensive, because these interfaces may need to be built and maintained by in-house support teams, but the lack of an instrument-LIS interface can result in inefficient and error-prone daily workflow in the laboratory. It has been demonstrated that manual entry of microbiology results is a source of laboratory errors (47,48), and other clinical laboratories have demonstrated that the development of in-house interfaces between instruments and the LIS can be useful in reducing manual entry errors and hands-on time (49,50). In order to optimize the efficiency and accuracy of all instrument testing, interfaces between laboratory instruments and the LIS should be employed for data transfer whenever possible.…”