lag-opt.github.io

Website for Optical Projection Tomography data from the Laser Analytics Group

This repository contains the most up-to-date version of OptiJ, an ImageJ plugin for denoising and reconstructing Optical Projection Tomography (OPT) data. Links to 3D visualizations of the data acquired using our open-source hardware and reconstructed using OptiJ can be found below. For any questions or comments, please contact Pedro Vallejo Ramirez, ppv23@cam.ac.uk.

To use the plugin, download the Opti_J.jar file and paste it into the plugins folder of your current version of Fiji/ImageJ. Restart imageJ, and OptiJ is ready for use!

Documentation for OptiJ can be found in the following repository: OptiJ documentation

The latest stable version of the source code (for further development or patches) can be found in: OptiJ source code

Sample data

5 individual lobes from adult murine lungs were extracted, dehydrated, stained, and cleared for OPT. Visualizations of the reconstructed data can be found in the following links. The open-source package FPBioimage (Fantham & Kaminski, Nature Photonics 2017) was used to render and share the reconstructed data.

  1. Left lobe, anti surfactant C
  2. Medial lobe, anti TFF1
  3. Medial lobe, anti TFF1, cropped
  4. Accessory lobe
  5. Left lobe, anti TFF1
  6. Superior lobe, anti TFF1

Videos

Links to youtube videos of the three first lobes in the previous section exploring the 3D morphology of the lung:

  1. Left lobe, anti surfactant C

  2. Medial lobe, anti TFF1

  3. Accessory lobe, anti TFF1