A simple toolbox of two ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.
Note: If you are not seeing this readme file at https://github.com/hansenjn/AdipoQ/ please visit this page to get the most recent version of and information about AdipoQ.
- AdipoQ_Preparator_-…-SNAPSHOT.jar (Download latest release here): An ImageJ plugin to segment objects (i.e., adipocytes, lipid droplets, nuclei) from background.
- AdipoQ_Analyzer_-…-SNAPSHOT.jar (Download latest release here): An ImageJ plugin to quantify objects (i.e., adipocytes, lipid droplets, nuclei) from a segmented image or a multi-channel image featuring at least one segmented chanenl.
- R markdown templates for post-hoc analysis are available here.
All the tools are optimized for studying adipocytes in stained tissue or in vitro after immunofluorescent labeling.
A comprehensive User Guide is available here.
In addition, we provide a quick-start and an example guide for analyzing cells and histological samples.
- Quick-start guide that teaches you the most important information for a first try of AdipoQ on an image of cultured cells.
- Example guide that walks you through the analysis of an example fluorescence microscopy image of cultured adipocytes using AdipoQ. The images used in the guide can be downloaded here:
- Soon we will provide here also a quick-start guide for using machine-learning (StarDist)-based predictions to detect nuclei in AdipoQ. Meanwhile, please read the notes on StarDist in the main user guide.
- Quick-start guide that teaches you the most important information for a first try of AdipoQ on an image of HE-labeled adipose tissue.
- Example guide that walks you through the analysis of an example image of HE-labeled adipose tissue with AdipoQ. The image used in the guide can be downloaded here:
When using any of the AdipoQ plugins or R scripts, please cite the following preprint:
Katharina Sieckmann, Nora Winnerling, Mylene Huebecker, Philipp Leyendecker, Dalila Juliana Silva Ribeiro, Thorsten Gnad, Alexander Pfeifer, Dagmar Wachten, Jan N. Hansen. AdipoQ—a simple, open-source software to quantify adipocyte morphology and function in tissues and in vitro. Molecular Biology of the Cell 2022, 33:12. doi: https://doi.org/10.1091/mbc.E21-11-0592
The source code for the plugins is available in the repositories for the individual plugins:
If you encounter problems, error messages, or would like to suggest / contribute new functions please use the issue systems on the respective repositories or send an email to jan.hansen (at) uni-bonn.de.
Copyright (C) 2019-2023: Jan N. Hansen.
AdipoQ has been developed in the research group Biophysical Imaging, Institute of Innate Immunity, Bonn, Germany (Lab Webpage).
Contacts:
- jan.hansen (at) uni-bonn.de
- dwachten (at) uni-bonn.de
The plugins are published under the GNU General Public License v3.0. A copy of the license is contained in this repository.