Open-source free software for image segmentation and labeling

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4 min readFeb 11, 2021
Image segmentation

You can make your own segmentation and/or labeling tool. I have my own image annotation tool and many of my colleagues have such software on MATLAB and Python. It’s a good programming practice to do it by yourself or improve on an existing one. You’ll know a lot during software development! However, it is time-consuming, especially for advanced functional and it is not related with Machine Learning experience.

This is why I have compiled a list of open source segmentation and labeling tools as of early 2021. I’ve not tested all of them, but only a few. See a review of my most favorite apps at the end of this article.

Actually, there are 758 public repositories on GitHub marked as annotation tool. I’ve just publish a several links from the top-rated. Also see awesome data labeling list of tools and useful links below.

Image segmentation tools

Online

I find that all online web-based tools are more convenient to work with. No installation required.

Local installation

  • LabelMe — MIT license. Source code with installation instructions. Another LabelMe tool.
  • Sefexa — Semi-automatic image segmentation.
  • Label tool — MIT license. See online demo without savings.
  • Django Labeller — MIT license. A light-weight image labeling tool for Python designed for creating segmentation data sets.
  • COCO Annotator — web-based image annotation tool (getting-started) designed for versatility and efficiently label images to create training data for image localization and object detection.
  • GIMP — GNU Image Manipulation Program. Open source alternative to Adobe Photoshop.
  • DeepMask and SharpMask — BSD license. Object proposal algorithms based on pretrained models. Automatic (not manual) segmentation. Has been archived by the owner, seems deprecated. MAC OS X or Linux.
  • MultiPathNet — BSD license. Automatic (not manual) segmentation. Seems deprecated. Linux.
  • Weka plugin — The Trainable Weka Segmentation (see wiki and video) is a Fiji plugin that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentation. Weka (Waikato Environment for Knowledge Analysis) can itself be called from the plugin.
  • Remo — Community free. Pip or Docker local installation.

Video

  • UltimateLabeling — A multi-purpose Video Labeling GUI in Python with integrated SOTA detector and tracker. MIT license.
  • VATIC — Deprecated, see CVAT.

Medicine segmentation tools

Segmentation software designed for 3D medical images and for medical image file formats.

  • MedSegOnline web app for radiology images. Free and simple volume segmentation of organs, tissue and pathologies in radiological images. You can segment the images manually, or let AI models do it for you. Besides there is also a list of external medical datasets: general databases and the cancer imaging archive (TCIA).
  • BioImage Suite Web — Web-based open-source (manual) medical image analysis suite primarily geared towards Neuroimaging Analysis.
  • Biomedisa — Free and easy-to-use open-source platform for segmenting large volumetric images, e.g. CT and MRI scans.
  • RIL-Contour — BSD type license. Python based, multi-platform. The toolkit consists of an imaging viewer with a wide range of capabilities for annotating medical images.
  • 3D slicer — For radiological images.
  • ITK-SNAP — GPL3 license. Multi-platform.
  • MITK — Free and versatile open-source software project for the development of medical image processing applications. It can be used as a C++ toolkit or application framework for software development.

Image labeling tools

Free image labeling tools (not segmentation) for object detection tasks. There are many more on GitHub.

Paid software

There is huge and intense competition between private companies in this area.

Review of my most favorite apps

The best labeling tool for me is, of course, my own software (one, two, three) :-). However, my own tools are not universal and without automation.

I’ve used LabelImg several times and it is OK for manual labeling with rectangles.

CVAT seems to be the leading open-source video and image annotation tool.

Besides price, functions and project management there is one new important parameter — automation using AI and classical algorithms for faster manual annotation process. Pay attention to automation when choosing your working tool.

Maybe in the near future I’ll try Groundwork, an online free image labeling tool for creating custom training datasets from satellite imagery. However maps are loading quite slowly.

Useful links

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