Dataset Information

A modular software framework for the design and implementation of ptychography algorithms.

ABSTRACT: Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this article, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential for designing new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.

SUBMITTER: Guzzi F

PROVIDER: S-EPMC9454962 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A modular software framework for the design and implementation of ptychography algorithms.

Guzzi Francesco F Kourousias George G Billè Fulvio F Pugliese Roberto R Gianoncelli Alessandra A Carrato Sergio S

PeerJ. Computer science 20220725

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this article, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicit ...[more]

PMID: 36091984

Similar Datasets

Project description:We designed a strategy for microarray analysis that is based on the identification of transcriptional modules formed by genes coordinately expressed in multiple disease data sets. Mapping changes in gene expression at the module level generated disease-specific transcriptional fingerprints that provide a stable framework for the visualization and functional interpretation of microarray data. The first step of the module-construction process analyzes expression patterns of transcripts across samples for individual diseases: sets of coordinately expressed transcripts were identified with an unsupervised clustering algorithm; in this case, the GeneSpring Version 7.1 (Agilent) implementation of the K-Means algorithm (k = 30). All transcripts detected in at least one sample were used as input; no screening for differential expression was performed. The second step of the module-construction process analyzed the “clustering behavior” of transcripts across diseases, taking into account the possibility that genes may cocluster in some diseases but not in others. Also, in our example, the transcripts that clustered together across all eight diseases were grouped to form a set of modules (round 1 of selection), and the stringency of the analysis was then decreased gradually to identify transcripts that belong to a similar K-means cluster in only a subset of diseases (round 2: seven out of eight diseases; round 3: six out of eight diseases). It is important to note that the module-selection process is “data-driven” and does not involve manual selection of genes by the investigator. We implemented the module-construction strategy described above, using as input a total of 239 peripheral-blood mononuclear cell (PBMC) samples obtained from individuals with one of the following conditions: systemic juvenile idiopathic arthritis (n = 47), systemic lupus erythematosus (n = 40), type I diabetes (n = 20), metastatic melanoma (n = 39), acute infections (Escherichia coli [n = 22], Staphylococcus aureus [n = 18], Influenza A [n = 16]) or liver-transplant recipients undergoing immunosuppressive therapy (n = 37). Transcriptional profiles were generated with Affymetrix U133A and U133B GeneChips (> 44,000 probe sets). A total of 4742 transcripts, distributed among 28 sets, were selected after running of the module-construction algorithm described above. Each module is assigned a unique identifier indicating the round and order of selection (i.e., M3.1 is the first module identified in the third round of selection). The stringency of this algorithm was tested statistically by implementation of the same module-construction procedure after randomization of the original data set. This process was repeated 200 times, without a single module identified. Therefore, the analysis of gene-cluster membership across multiple diseases provided a stringent means to identify PBMC transcriptional modules.

Project description:BackgroundRegular physical activity is proven to help prevent and treat noncommunicable diseases such as heart disease, stroke, diabetes, and breast and colon cancer. The exercise data generated by health and fitness devices (eg, treadmill, exercise bike) are very important for health management service providers to develop personalized training programs. However, at present, there is little research on a unified interoperability framework in the health and fitness domain, and there are not many solutions; besides, the privatized treadmill data transmission scheme is not conducive to data integration and analysis.ObjectiveThis article will expand the IEEE 11073-PHD standard protocol family, develop standards for health and fitness device (using treadmill as an example) based on the latest version of the 11073-20601 optimized exchange protocol, and design protocol standards compliance testing process and inspection software, which can automatically detect whether the instantiated object of the treadmill meets the standard.MethodsThe study includes the following steps: (1) Map the data transmitted by the treadmill to the 11073-PHD objects; (2) Construct a programming language structure corresponding to the 11073-PHD application protocol data unit (APDU) to complete the coding and decoding part of the test software; and (3) Transmit the instantiated simulated treadmill data to the gateway test software through transmission control protocol for standard compliance testing.ResultsAccording to the characteristics of the treadmill, a data exchange framework conforming to 11073-PHD is constructed, and a corresponding testing framework is developed; a treadmill agent simulation is implemented, and the interoperability test is performed. Through the designed testing process, the corresponding testing software was developed to complete the standard compliance testing of the treadmill.ConclusionsThe extended research of IEEE 11073-PHD in the field of health and fitness provides a potential new idea for the data transmission framework of sports equipment such as treadmills, which may also provide some help for the development of sports health equipment interoperability standards.

Dataset Information

A modular software framework for the design and implementation of ptychography algorithms.

Publications

A modular software framework for the design and implementation of ptychography algorithms.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets