CellLocator by Allen Institute

Manually align specimens to annotated 3D spaces

Prerequisites

• Microsoft Windows 7 or above recommended

• Supported Microsoft Visual Studio versions:

  • Visual Studio 2015

• CMake, version 3.11 or above

• Qt, version 5.10 or above

• Git

• Subversion

• Setting up your git account:

  • Create a Github account.

  • Setup your SSH keys following these instructions at the exception of step 2 where you should NOT enter a passphrase.

  • Setup your git username and your git email.

  • If not already done, email Jean-Christophe Fillion-Robin <[email protected]> to be granted access to the BICCN/cell-locator repository.

Checkout

1. Start Git Bash
2. Checkout the source code into a directory C:\W\ by typing the following commands:

cd /c
mkdir W
cd /c/W
git clone https://github.com/BICCN/cell-locator.git cell-locator

Note: use short source and build directory names to avoid the maximum path length limitation.

Build

Note: The build process will take approximately 3 hours.

Option 1: CMake GUI and Visual Studio (Recommended)

1. Start CMake GUI, select source directory C:\W\cell-locator and set build directory to C:\W\cell-locator-rel.
2. Add an entry QT_QMAKE_EXECUTABLE pointing to C:\D\Support\qt-4.8.7-64-vs2013-rel.
3. Generate the project.
4. Open C:\W\cell-locator-rel\CellLocator.sln, select Release and build the project.

Option 2: Command Line

1. Start the Command Line Prompt
2. Configure and build the project in C:\W\cell-locator-rel by typing the following commands:

cd C:\W\
mkdir cell-locator-rel
cd cell-locator-rel
cmake -G "Visual Studio 14 2015 Win64" -DQT_QMAKE_EXECUTABLE:PATH=C:\Qt\5.9.1\msvc2015_64\bin\qmake.exe ..\cell-locator
cmake --build . --config Release

Package

Install NSIS 2

Option 1: CMake and Visual Studio (Recommended)

1. In the C:\W\cell-locator-rel\Slicer-build directory, open Slicer.sln and build the PACKAGE target

Option 2: Command Line

1. Start the Command Line Prompt
2. Build the PACKAGE target by typing the following commands:

cd C:\W\cell-locator-rel\Slicer-build
cmake --build . --config Release --target PACKAGE

Resources

• 3D Slicer Developer Wiki