Botelho Hugo
Tischer Christian
Execution Platform
Implementation Type
Programming Language
Supported image dimension
Interaction Level

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.

Entry Curator