Skip to content
Snippets Groups Projects
Select Git revision
  • ea38a304bea870cf4a6d6b25c4ffb932a7a5480c
  • master default protected
2 results

leversc

user avatar
leversc readme link format update
ac (tb) authored
ea38a304
History
user avatar ea38a304
History
Name Last commit Last update
docs
sampleImages
src
.gitattributes
.gitignore
license.txt
readme.md
readme.md

LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images

LEVERSC is a cross-platform multichannel 3-D visualization tool for volumetric fluorescent images such as those produced by confocal or light-sheet microscopy.

Installation

You must install both the leversc app and the client. First, install the LEVERSC app for your operating system. Next, follow the instructions for integrating LEVERSC into your client of choice (ImageJ, Python, or MATLAB).

App Install

MacOS App Install

Windows App Install

Linux App Manual Install

  1. Download the Linux Appimage.
  2. Symlink the appimage file to a folder in $PATH (e.g. ~/.local/bin). 
    ln -fs /path/to/leverjs-*.AppImage  ~/.local/bin/leverjs

Client Install

ImageJ Plugin

  1. First, install the leversc app

  2. Download the ImageJ plugin.

  3. Copy the plugin jar file to the plugins/3D folder in your ImageJ executable directory.

  4. The plugin will appear in the ImageJ Plugins menu as Plugins->3D->Leversc Viewer

    Note: If using Fiji (highly recommended) then you may wish to create the 3D subfolder in plugins and place the jar file within, as it can make it easier to find. Alternatively, the jar file can be placed directly in the plugins folder and will be listed in the Fiji menu as Plugins->Leversc Viewer.

Python Module

  1. Download the Python module directory (Select the download icon and choose Download this directory).
  2. Extract the downloaded Python folder to a convenient location.
  3. Add the folder to your PYTHONPATH environment variable so that import leversc statements can automatically find the LEVERSC module

MATLAB Class

  1. Download the MATLAB class directory (Select the download icon and choose Download this directory).
  2. Extract the downloaded MATLAB class and support folders to a convenient location.
  3. Add the folder to your MATLAB path, for example by adding the statement addpath('path/to/extracted/folder') to your startup.m file.

Basic Usage Examples

Fiji/ImageJ

  1. Download the sample OME TIFF image.

    NOTE: Fiji/ImageJ will not be able to open the HDF5 format sample image that ships with LEVERSC. Be sure to use the OME TIFF.

  2. Choose Open... in Fiji and navigate to the downloaded image (or another dataset).

  3. Once the image has loaded, select Plugins->3D->Leversc Viewer, this should launch the LEVERSC program and load the image data for the selected frame.

Python

  1. Download or clone the full LEVERSC repository
  2. Navigate to the LEVERSC src/Python folder.
  3. Run: python test_leversc.py.

MATLAB

  1. Download or clone the full LEVERSC repository
  2. Launch MATLAB and navigate to the leversc src/MATLAB folder.
  3. In the MATLAB terminal, run: sampleRotateVolumeMovie.

Debugging Tips

  1. Be sure your firewall isn't blocking the LEVERSC visualization tool from communicating. This should not be an issue in most cases. With the LEVERSC viewer running, open a web browser window. Enter 'http://localhost:3001/info'. If you get an error, check your firewall and be sure there are no LEVERSC specific rules, and that your localhost (loopback) connections are enabled.
  2. Examine any errors or warnings from the LEVERSC visualization tool. From the View menu, choose 'toggle developer tools'. Select console. Any debug output here can be submitted as part of a bug report.

Bug Reporting

Please submit any bugs or issues via email to andrew.r.cohen 'at' drexel.edu. Mark the subject line as 'leversc bug report'. Include your operating system and version, what client you are using (e.g. MATLAB, Python, ImageJ), and any debug output.

Further Details

Details of the LEVERSC tool architecture and API can be found in the online API documentation. A detailed usage example is available here, and a step-by-step guide for implementing a plugin to communicate with LEVERSC through the API is provided here.

The source code for LEVERSC integrations are available in this repository (ImageJ plugin, Python module, MATLAB class).

Additionally, the node.js and webgl source code for the LEVERJS/LEVERSC tool, as well as build instructions are available in the main leverjs repository.