KNIME includes a Database Reader node that can access CellProfiler-produced data. KNIME (University of Konstanz) is an open source modular data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. The IN Cell Analyzer acquisition software from GE Healthcare generates customizable CSV reports in a format that allows CellProfiler to import images and metadata via the LoadData module. IN Cell Analyzer automated cell imaging systems yield morphological and molecular data via high content imaging and analysis. GenePattern (Broad Institute) is open source software that gives a broad audience access to a growing repository of sophisticated analytic tools for genomic data, while an API supports computational biologists.ĬellProfiler can format and export image-based data as a GenePattern GCT file (.gct) through the ExportToSpreadsheet module or data tool. Using CellProfiler and FCS Express 4 Image Cytometry: joint webinar with DeNovo Software on using CellProfiler to peform basic image assays and generate data compatible with export into FCS Express. The image cytometry version allows the user to review and analyze multi-parametric data sets and relate results back to the original images.įCS Express 4 software can import comma-delimited files produced by the CellProfiler ExportToSpreadsheet module or data tool. These tools can read comma- or tab-delimited files generated by the CellProfiler ExportToSpreadsheet module or data tool.įCS Express 4 Image Cytometry (De Novo Software) provides population based analytical tools common in flow cytometry. Calc (LibreOffice) is open-source software and freely-available. Excel (Microsoft) is a general business comercial package, whereas Prism (Graphpad) is a commercial program tailored towards research scientists for statistical analyses. Spreadsheet programs like these are useful for plotting small amounts of data. Using the final building block (Define Results) of a Columbus analysis routine, data can be exported in a format that CellProfiler Analyst can read. The Columbus system (Perkin Elmer) is a universal high-volume image data storage and analysis system that brings access to images from a wide range of sources including all major high content screening instruments via the Internet. Some details on using the component are provided here. The user can run a protocol and send images to be analyzed into CellProfiler as input, and allows for images and analysis data to be retrieved from CellProfiler for downstream data workflows enabled by AEP. The Pipeline Pilot Imaging Component Collection provides a component, 'CellProfiler (on Server)', for integration with CellProfiler. The Component Collections of the Accelrys Enterprise Platform (AEP) allows researchers to build, deploy, analyze and report on complex scientific data types within the Accelrys applications framework and other third-party applications. In addition to performing image analysis to generate measurements, CellProfiler has built-in tools in the Data Tools menu to generate a few types of plots.ĬellProfiler output files in MATLAB (.mat) and HDF5 (.h5) can be opened by CellProfiler's data tools.ĬellProfiler Analyst allows analysis, exploration and machine-learning for high-dimensional image-based data.ĬellProfiler Analyst can be used with data that follows a simple format: One image table with rows of databases produced in CellProfiler using the ExportToDatabase module or data tool. Software for analyzing CellProfiler-produced data Software
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |