Beholder is a Python end-to-end tool, microscopy image, and data analysis tool for biophysicists and synthetic biologists. With Beholder, researchers and microscope users can automatically obtain fluorescence measurements of a population of cells (at the single-cell level) for multiple experiments from their ND2 files.

 

Batches of independent microscopy experiments containing Phase-contrast and fluorescence images for multiple timestamps (usually hundreds of Gbs) are first automatically organized and converted into TIFF files. The `Beholder` command uses a particular JSON file called a run-list that describes the pipeline stages, order, and arguments. Next, phase-contrast images are used for cell segmentation, and their corresponding fluorescence images are used for extracting relevant information at the single-cell level.

Beholder is written in Python, and all commands are run via the poetry environment at the top level of the code repository. The `beholder` command uses a particular JSON file called a run-list that describes the pipeline stages, order, and arguments. This way, the files of the batch and the steps and actions desired for the analysis (in case one wants to skip some of them) are defined within run-lists by the user before the analysis.

Key Features

  • Convert the input ND2 files (Nikon) into TIFF files

  • Perform cell segmentation and labeling to the TIFFs to find cell contours and determine single cell coordinates

  • Fluorescence image alignment to extract pixel intensities from single cells

  • Upload this data to a remote server (analysis done remotely)

  • Repository to store batch processing run-lists for Beholder

  • Download analysis results locally while keeping images stored in the server

Funding

  • Living Computing Project

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Beholder is free to use. Follow the installation instructions below to install.

Screen Shots

Beholder1.jp2