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Copyright (C) 2020 RIKEN

Sample codes and tools for reading and writing BD5 file format

  • This repository contains the sample source codes for reading and writing BD5 file formats using Python in Juypter notebook.
  • The samples include codes using either the h5py or pytables packages.

Sample codes in Juypter notebook:

Sample codes for writing BD5 object entities:

BD5 object entities

  • Writing out object entities, line, point, circle, sphere and face.
    • BD5write_numpy (uses h5py) with explanation
      • Writing line, face, sphere, point and circle objects as numpy array to BD5 files.
    • BD5write_circle_details (uses pytables) with explanation
    • BD5write_circle (uses pytables)
      • Reading in an image segmentation data stored in a TIFF image file, and write it as a circle in BD5 format.
    • BD5write_point (uses pytables)
      • Reading in an image segmentation data stored in a TIFF image file, and write it as a point in BD5 format.
    • BD5write_line (uses pytables)
      • Reading in an image segmentation data stored in a TIFF image file, and write it as a line in BD5 format.

Sample codes for writing BD5 files using h5py

  • CSVread_BD5write (uses h5py) with explanation
    • Reading in a BD5 file and writing out a CSV file/Reading in CSV file and writing out a BD5 file
  • BD5write_numpy (uses h5py)
    • Writing line, face, sphere, point and circle numpy arrays to BD5 files
  • BD5append_trackinfo_point (uses h5py) with explanation
    • Reading in a BD5 file with time series information. It tries to calculate and track the objects over two time points and then append the trackInfo information to a BD5 file.
  • BD5read_count (uses h5py)
    • Reading in an existing BD5 file and do some simple analysis by counting the number of nuclei vs time point and plotting out a proliferation curve of C.elegans.
  • BD5read_displacement (uses h5py)
    • Reading in an existing BD5 file and do some simple analysis by calculating the displacement of ABal nucleus of C.elegans

Sample codes for writing BD5 files using pytables

  • BD5write_circle_details (uses pytables) with explanation
  • BD5write_circle (uses pytables)
    • Reading in an image segmentation data stored in a TIFF image file, and write it as a circle in BD5 format.
  • BD5write_point (uses pytables)
    • Reading in an image segmentation data stored in a TIFF image file, and write it as a point in BD5 format.
  • BD5write_line (uses pytables)
    • Reading in an image segmentation data stored in a TIFF image file, and write it as a line in BD5 format.
  • BD5write_timeseries_point (uses pytables) with explanation
    • Reading in two time series ROIs data stored in TIFF image files, and track the objects over the two time points and write that to a BD5 file.

BD5 manual

Detailed description can be found on the link below. http://ssbd.qbic.riken.jp/bdml/bd5.html

Reference

BD5: an open HDF5-based data format to represent quantitative biological dynamics data Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami bioRxiv 2020.04.26.062976; doi: https://doi.org/10.1101/2020.04.26.062976