• Install Anaconda or Miniconda
  • Launch the Anaconda PowerShell Prompt in Windows or the terminal in macOS/Linux. Create a new conda environment with a custom name, such as seg2link-env, and activate it by running following commands:
$ conda create -n seg2link-env python=3.8 pip
$ conda activate seg2link-env
  • Install Seg2Link:
(seg2link-env) $ pip install seg2link

Data preparation

Before performing segmentation, you must have at least the following data:

  1. A 3D cell image saved in a folder as a set of 2D Tiff images.
  2. A cellular/non-cellular prediction based on 1, saved in a different folder as 2D Tiff images.
  • Activate the created environment and launch Seg2link:
$ conda activate seg2link-env
(seg2link-env) $ seg2link

  • Screenshots

    start_seg2link

    Note I used an environment name seg2link rather than seg2link-env.

    choose_round

    An initial interface is displayed.

Choose a module

  • Choose a proper module from the initial interface to perform:
    • the semi-automatic segmentation (in Module Seg2D+Link)
    • or the comprehensive 3D inspection and corrections (in Module 3D correction)