Biom3d

Congrats! You’ve just found Biom3d, an easy-to-use tool for volumetric image semantic segmentation.

This tool is addressed to three different profiles:

• Non Programmers, who could be interested to use the Graphical User Interface (GUI) only. After going through the installation [link], start with [Quick Run/GUI].

• Python Programmers, who could be happy with some minimal customization, such as adapting Biom3d to a novel image format or choosing another training loss. After going through the installation [link], start with [CLI].

• Deep Learning Programmers, who are not scared of digging in some more advanced features of Biom3d, such as customizing the deep learning model or the metrics. After going through the installation [link], start with the basic here [CLI] and then go directly to the tutorials [link].

Installation

• Installation
  • Graphical User Interface
  • Application Programming Interface
  • Source code

Tutorials

• The Graphical User Interface
  • Splash screen
  • Preprocess & Train
  • Predict
• The Command Line Interface
  • The quickest way
  • Train with your own images: another example with tif files
  • Preprocess first, train after
  • Evaluate
  • Omero prediction
  • Even more

FAQ

• Frequently asked questions
  • “FileNotFoundError: [Errno 2] No such file or directory” or “FileNotFoundError: [Errno 2] No such file or directory”
  • NaN loss

API

• Preprocessing
  • Preprocessing
• Auto-configuration
• Builder
• Metrics
• Callbacks
• Trainers
• Predictors