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Welcome to LightSuite

LightSuite is a MATLAB-based pipeline designed for the registration and analysis of large-scale microscopy datasets. It provides modular workflows for whole-brain lightsheet volumes, coronal slice series, and spinal cord data, bridging the gap between raw microscopy images and anatomical reference atlases (CCF).

What can I do with LightSuite?

LightSuite automates the complex tasks of mapping experimental data to standard anatomical coordinates and quantifying labeled cells.

  • Whole-Brain Lightsheet Analysis: Process continuous 3D volumes. The pipeline handles preprocessing (median filtering, binary conversion), automated cell detection (SNR-based local maxima), and registration to the Allen Brain Atlas.
  • Spinal Cord Analysis: Specialized tools for straightening and registering spinal cord volumes. It includes a dedicated GUI for defining the central canal and anterior/posterior axes to unroll and map the cord before registration.
  • Slice Analysis: Optimized for conventional wide-field microscope data (e.g., coronal slices). It registers individual 2D planes to the atlas and outputs registered image stacks and cell coordinates.
  • Probe & Implant Tracing: Localize Neuropixels probe tracks and cylindrical implants (optical fibers / GRIN lenses) on a registered brain, exporting their atlas-space trajectories and the regions they pass through (AP_histology-compatible probe_ccf).

Hardware Requirements

  • Standard Workstations: The Slice Analysis module is optimized for efficiency and has been tested on standard computers without GPUs.
  • High-Performance Workstations: For Large-scale lightsheet volumes, we recommend a system with a dedicated GPU to accelerate 3D operations (such as spatial band-pass filtering and cell detection).

Supported Data Formats

1. Large-scale Lightsheet Volumes

The pipeline accepts axially-sliced data as a series of single-channel 2D TIFF planes, as multi-channel volume TIFFs, or as per-channel volume TIFFs split across files. Support for other brain orientations is planned.

2. Spinal Cord Data

We support low-resolution whole cord volumes. Channels can be stored within the same TIFF volume or separated.

3. Slice Volumes

We support:

  • A series of 2D TIFF planes (one file per slice).
  • Direct output from AxioScan scanners (.czi files).

Getting Started

  1. Installation: Follow the instructions in Installation to set up MATLAB dependencies and external tools (Elastix).
  2. Understand the pipeline: Skim How it works for the shared registration and cell-detection concepts that all workflows build on.
  3. Configuration: LightSuite uses script-based configuration. You will adjust parameters (such as cell diameter or file paths) directly within the analysis scripts.
  4. Select your Workflow: