High content screening

CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data. Within shinyHTM the user is guided through a linear workflow which follows the following best practices:

• Inspect the numerical data through plotting
• Measurements are linked to raw images
• Perform quality control to exclude images with aberrations or where image analysis failed
• Perform a reproducible data analysis
• Normalize data and report statistical significance

Image visualization relies on Fiji/ImageJ, along with its wealth of analytical tools.

shinyHTM can be used to analyze image features obtained with CellProfiler, ImageJ or any other bioimage analysis software. The output of analysis is a publication-ready scoring of the data.

shinyHTM is based on the R shiny package.

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

The recent version requires images of a lateral position. It is important that the position is precise since deviation may confound with feature annotations. Images from any source can be used. However, depending on the image properties parameters may have to be adjusted. Furthermore, images obtained with normal microscope and not using an automated position system with embryos in glass capillaries require conversion using a KNIME workflow (the workflow is available as well). As a result of the analysis the software provides JSON files that contain the coordinates of the features. Coordinates are provided for eye, fish contour, notochord , otoliths, yolk sac, pericard and swimbladder. Furthermore, pigment cells in the notochord area are detected. Additional features can be manually annotated. It is the aim of the software to provide the coordinates, which may then be analysed subsequently to identify and quantify changes in the morphology of zebrafish embryos.