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OMERO.searcher
An extension of the OMERO.web client that provides the ability to search for images by their content (e.g., subcellular patterns) rather than just by their annotations. It was developed by the Murphy group at Carnegie Mellon University. OMERO.searcher 1) finds images whose content, as reflected by subcellular location image features, is similar to one or more query images, 2) can use positive and/or negative examples 3) can be iterative, meaning it allows the user to refine the search results (a process referred to as relevance feedback).
Planform / Planarian formalization
A manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. Planform contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset.
ImageJ-MATLAB
A Java library facilitating bi-directional interoperability between MATLAB and ImageJ applications. ImageJ-MATLAB provides an extensible and bidirectional bridge for mutual exchange of data between these two environments. The foundation of ImageJ-MATLAB consists of two Converter plugins: enabling ImageJ Datasets and MATLAB matrices to be freely exchanged within the SciJava framework. Both directions of conversion use the third-party MATLABControl library to manage interaction with a MATLAB instance.
CGE / Circadian Gene Expression
Automatically tracks moving cells over longer period of time. CGE consists of two ImageJ plugins: (1) CGE_Preprocessor that precomputes all data required for the recording, and (2) CGE_Recorder that uses the data produced by the first plugin and interacts with the user to determine the trajectory and the outline of a nucleus. The software allows one to study the different features and changes of cells with significantly varying locations and protein expression levels imaged over a period of several days.
WormGender
A software package for automatic phenotyping in C. elegans included in QuantWorm. WormGender is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements.
phenomeImpute
Imputes missing values in large-scale high-dimensional phenome data. phenomeImpute contains four variations of K-nearest-neighbor (KNN) methods and was compared with two existing methods, multivariate imputation by chained equations and missForest. The four variations are imputation by variables (KNN-V), by subjects (KNN-S), their weighted hybrid (KNN-H) and an adaptively weighted hybrid (KNN-A). The results show that Imputation of missing values with low imputability measures increased imputation errors greatly and could potentially deteriorate downstream analyses.
PRECOG / PREsentation and Characterization Of Growth-data
Automates visualization, analysis and exploration of complex and highly resolved microbial growth data. PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. It filters the raw optical densities in a three-step procedure to remove or reduce noise and bias. PREGOG’s data filtering has been tested by comparing its performance to a multi-layered neural networks noise reduction filter.
flippant
Analyses data in the context of dithionite scramblase assays. flippant allows to analyze data from statistical computing and graphics and arrives at publication-grade graphics that offer extensive facilities for individual optimization and adaptation. It provides a platform for review, dissemination and extension of the strategies it employs. The tool was tested by reanalyzing a subset of data. It shows identical trends and close matches of the results, supporting identical conclusions.
Biosensor Processing
Allows processing raw ratiometric biosensor images into fully corrected "ratio maps" or "activation maps” - images. Biosensor Processing includes, for quantitative widefield imaging of ratiometric biosensors, application of all necessary image corrections needed. This tool follows a 6-steps procedure: (i) shading correction; (ii) background subtraction; (iii) image masking; (iv) automated image registration; (v) image shear, rotation and scaling correction; and (vi) ratio calculation.
hctsa / Highly Comparative Time-Series Analysis
A software package for running highly comparative time-series analysis. hctsa automates the selection of quantitative phenotypes from time-series data by leveraging a large and interdisciplinary literature on time-series analysis. hctsa allows thousands of time-series analysis features to be extracted from time series (or a time-series dataset), as well as tools for normalizing and clustering the data, producing low-dimensional representations of the data, identifying discriminating features between different classes of time series, learning multivariate classification models using large sets of time-series features, finding nearest matches to a time series of interest, and a range of other visualization and analysis functionality.
SC-QI / Structural Contrast-Quality Index
Explores effective features that are consistent with the characteristics of a human visual system (HVS) for visual quality perception. Image quality assessment (IQA) is a computational method that adoptes a structural contrast index (SCI), which can well characterize local and global visual quality perceptions for various image characteristics with structural-distortion types. It tends to adaptively characterize perceived visual quality for different image texture characteristics with structural-distortions types where the structural-distortion is defined as a distortion due to change in inter dependency among neighbour pixels.
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