itisfoundation/osparc-iseg

The Medical Image Segmentation Tool Set (iSEG) is a fully integrated segmentation (including pre- and postprocessing) toolbox for the efficient, fast, and flexible generation of anatomical models from various types of imaging data

Description

The Medical Image Segmentation Tool Set (iSEG) is a fully integrated segmentation (including pre- and postprocessing) toolbox for the efficient, fast, and flexible generation of anatomical models from various types of imaging data. iSEG includes a variety of semi-automatic segmentation methods. The key strengths of iSEG are a) a powerful set of tools for manual segmentation (correction), b) support for massive image sizes, c) suport for segmenting complex models with a large number of tissues, e.g. for inserting thin layers. It is the only powerful segmentation platform, which supports color images, e.g. from the NIH Visible Human or Visible Korean projects.

iSEG features a plugin mechanism, which allows users to easily extend the application with custom widgets. The development of iSEG has been driven by the Virtual Population project at the IT'IS Foundation, due to a lack of alternatives amongst open source and commercial tools.

Compilation instructions

A defined set of 3rd party libraries are required in order to compile iSEG. Instructions as to how these libraries must be installed and compiled are provided below.

Required applications

The applications below are needed in order to compile iSEG and its dependencies.

• CMake: 3.12 minimum
• C++14 compiler
• Git

Required 3rd party libraries

The libraries below are required to be compiled and installed on the system in order to compile iSEG. Platform specific instructions for each library are given below.

• Boost, Boost license
• HDF5, BSD-like license
• ITK, Apache 2.0 license
• VTK, BSD license
• Qt 4.8, GPL3 and LGPL2.1 license
• EIGEN MPL2 license

Note

For installing EIGEN just download and extract the source code

Compiling iSEG

• Windows/Visual Studio instructions
• MacOS/Clang++ instructions
• Ubuntu github action
• With Docker images instructions

osparc-iseg's Issues

Add log window

info, warning and error messages are currently written to a log file, but are not visible to user.

add window, which shows these messages, and allow to configure if error messages trigger popup (message window).

Get rid of Qt3Support Module

In order to allow iSEG to switch to Qt5, we need to get rid of Qt3Support.
The main use of Qt3Support is the layout of widgets and possible in some legacy API functions, like isOn vs isChecked.

child of ITISFoundation/osparc-simcore#580

Collapsible parameter view for widgets

The widget selection view and widget parameter view currently use too much space. While you are working with a widget/tool you often don't need to see either.

It would be nice if the widget related views could be conveniently collapsed/uncollapsed (or easily closed and opened).

Images subfolder is not being copied on linux build

This is only enabled for APPLE and MSVC. Simple fix but for now the osparc service does that manually.

Add Python interface, console and script runner

maybe use ideas from https://github.com/OpenGP/starlab/tree/master/core/plugins/gui_python/pythonqt

Wrap ITK progress into a progress view

Split disconnected tissue regions creates empty regions

Simplify UI of iSEG

Usability feedback of iSEG suggests that simplifying the UI will largely improve the user experience.

In my experience, showing by default only some sub-windows would be a good first step. What do you think @esraneufeld, @newton1985? If that is good, which ones?

cc @mguidon