hansenjn/adipoq

A simple toolbox of ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.

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.

Tools

• 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.

How to use?

A comprehensive User Guide is available here.

In addition, we provide a quick-start and an example guide for analyzing cells and histological samples.

Analysis of cultured cells - guides

• 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:
  • Day4-FI_Sh_s37.tif
  • Day0-ctrl_Sh_s174.tif
• 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.

Analysis of histological images - guides

• 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:
  • WT CD Test.tif

How to cite?

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

Source code and issues

The source code for the plugins is available in the repositories for the individual plugins:

• AdipoQ_Preparator GitHub repository
• AdipoQ_Analyzer GitHub repository

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

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

Licenses

The plugins are published under the GNU General Public License v3.0. A copy of the license is contained in this repository.