Getting Started

Installing Cell Locator

Download the latest release on GitHub

System Requirements

Cell Locator is based on 3D Slicer, so refer to the 3D Slicer System Requirements.

Cross-platform Availability

Installers are only generated for 64-bit Windows, however it is possible to build Cell Locator from source on any platform which supports 3D Slicer.

Refer to the Cell Locator build instructions.

Using Cell Locator

Quick Start

After starting Cell Locator, you will choose an atlas.

Atlas Selection Startup Dialog

After selecting an atlas, the application is ready with an annotation named Curve already created.

Before adding points to the annotation:

  1. Switch to Edit interaction mode.

  2. Use the reformat widget available in the 3D viewer on the right to update the orientation and identify a slice plane of interest.


Alternatively, you may directly set the the raw, pitch and yaw angles.

You can switch to Place interaction mode and start adding points to the annotation.

  1. Left-Click to add (or place) points.

  2. Right-Click to switch back to the Edit interaction mode.

Once you are done adding points, you can update annotation properties.

  1. Switch the annotation type from Spline to PolyLine.

  2. Renane the extension.

Finally, you can save the annotation as a .json file by clicking on the Save button.

User manual

Browse the Application Overview section to learn about the application user interface.