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).
Gathers various modular functions for analyzing plants images. PlantCV is an open and community-based software providing a library of Python scripts that can be used for various features such as quantitative processing, normalization or leaf segmentation as well as for the construction of processing pipelines. It aims to be a flexible platform that permits the analysis of data from several plant phenotyping systems.
Aligns linearly correlated signals or images. The RASL solution builds on advances in rank minimization and formulates the batch alignment problem as the solution of a sequence of convex programs. The algorithm achieves pixelwise accuracy over a wide range of misalignments. This tool serves as a preprocessing step for a training set of images.
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.
Allows exploration, analysis and interpretation of single-cell data. Vizardous’ core functionality is to visualize time-resolved, single-cell and population data. It can be used for the automated analysis of data as well. With Vizardous, lineage tree drawings can be upgraded with various, time-resolved cellular characteristics. Associated statistical moments link single cell and the population-average level.
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.
Detects patch-based carcinoma in confocal laser endomicroscopy (CLE) images. This patch probability fusion method that can provide additional real-time information about the suspicious lesion, supportive to the clinical examination. The software can serve as an additional tool supporting the biopsy and the following histopathological examination. It was applied on CLE images of oral squamous cell carcinoma (OSCC).
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.
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.
Provides accurate scores of a colony size across a very wide range of sizes, including very small ones that might not be picked up at all by imaging-based approaches. PHENOS combines multiple output files from the microplate readers and automatically generates a variety of data visualizations, and output files containing various growth curve summary values. It also offers a viable approach to growth phenotyping.
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.
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.
Automates the characterization of dye decolorization in fungal strains. DecoFungi is based on a transfer learning method that uses the output of a deep neural network to train a complete classifier for the target task. It allows to: analyze an image, analyze an image with its control image, analyze a zip file, and analyze a zip file containing a control image. This tool decreases the burden and subjectivity of visually classifying the dye decolorization level.
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.
Serves for large-scale plant species identification. DWSRC allows users to recognize plant species. It can generate discriminative sparse codes that can be used to represent the test sample by combining both linearity and locality information for improving recognition performance. It aims to exploit the locality and similarity of the original dataset and the test samples by sparsely representing the test samples.
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.
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.
Deduces microbial mutation rates from fluctuation assay data. rSalvador is a R package that provides various computational method for computing maximum likelihood (ML) estimates and likelihood ratio-based confidence intervals. The application can also be used to compare mutation rates using likelihood ratio tests and to compute mutant cell distribution and plot log-likelihood functions, simulate fluctuation experiments as well as determine sample size.
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.
Smoothes an image without altering its edges. BEEPS is an ImageJ plugin that consists in a version of the bi-exponential filter with adaptive weights. The software performs edge-preserving smoothing, while producing results that closely mimic those of the bilateral filter. It transforms an input image into an output image of the same size.
Allows exploration and analysis of analytical microscopy data. ScatterJn handles more than two input images (or image stacks, respectively) by creating a matrix of pairwise scatterplots. It offers the possibility to manually classify pixels by selecting regions of datapoints in the scatterplots as well as in the spatial domain. The tool can potentially be of use in any situation that requires exploration of quantitative image data.
Offers a wrapper developed for The Cancer Imaging Archive (TCIA) REST API. TCIApathfinder is a R package that gives access to the database through a R environment. It includes some features allowing to browse the full collection and to select patients for analysis. Additionally, the program allows users to import images and supporting data into R scripts with the aim of performing further analysis thanks to additional packages.
Creates CPK coloring, Ball and Stick and worm pictures of molecules. QTree is able to generate near-photographic quality images though it does not generate shadows. It offers functions to colouring by residue type, atom type, chain, temperature factor, or residue range, rotation, background colouring, modified lighting models and slabs through the structure.
Provides a method for context aware image manipulation. CAIM focuses on content aware image resizing and object removal. The technique implemented in this application uses dynamic programming to identify a seam (a set of connected pixels on a single image from top to bottom or from left to right). It sets the value of the pixels corresponding to that object to very small values which forces the seams to pass through that object.
Allows users to create a database for managing life sciences images. INAVEO offers image archiving, reviewing, analysis in local and network mode. This software can handle images of any types and any sizes and supports import routine that enable to determine traceability data and rename images. Users can generate written and audio annotations on their images.
Provides a population structure and principal component analysis (PCA) viewer. Genesis is an application that allows users to interactively produce publication quality pictures. This program takes as input the output of PCA or admixture programs.
Provides educational tool for Fourier transform and its application in the field of digital image processing. FTutor is a program that aims to present and teache Fourier transform. The software (1) performs Fast Fourier Transform on a selected image, (2) displays its frequency spectrum, which users can modify using Brush tool, Rectangle tool, Ellipse tool or Filtering, and (3) performs Inverse Fast Fourier Transform to display the modification result.
Offers a platform dedicated to neural structures viewing. NeuroGL provides a graphic interface that allows users to navigate through a targeted structure by using both a set of instructions or just by click and drag. The software exploits files from the NeuroZoom software.
Provides streamlined data processing and analysis capability for developmental biology and disease modeling using zebrafish model. ZFIQ is a data analysis system that can deal with the diversity of zebrafish datasets and data quality. This platform includes four components: (i) a pipeline construction environment, (ii) a pipeline pool, (iii) the algorithm and method repository and (iv) the pipeline running environment.
Improves the group-lasso-based SCCA (Sparse Canonical Correlation Analysis) methods. TGL-SCCA is an algorithm that has the following advantages: (i) it performs better feature selection ability, but also can be solved effectively like the ℓ1-norm; (ii) it is an adaptive shrinkage method if τ is tuned appropriately; (iii) it can discriminate the small coefficients from large coefficients, and leave those large ones less penalized.
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