Quantification of vessel and vessel lumen area in tissue sections

Project Description

The aim of the project is to create an ImageJ macro that can be used to measure three different areas in confocal images of tissue sections; (1) the whole section area, (2) the vessel area and (3) the lumen area within the vessels. The researcher provides a .lif file with merged tilescan images in four channels: Channel 1: DAPI stain; Channel 2: GFP reporter; Channel 3: LYVE1 stain and Channel 4: VEGFR2 stain. An overlay of all four channels is used to measure the total area. From the overlay of all four channels, all the lumens (=areas with no staining) that are located within the vessels (Channels 3-4) is measured. An overlay of channels 3-4 are used to measure the vessel area. The macro creates a result folder containing a .csv file with the measurements, a TIF file with the maximum projection image and a TIF file with the masked measurement areas in RGB (see Figure above).


Project Information

  • BIIF Principal Investigators

    • Christophe Avenel
    • Petter Ranefall

    External Authors

    Bojana Jakic, Taija Mäkinen
  • Date

    2020-09-07 🠚 2020-09-18