Lipid Droplets Tool

The Lipid Droplets Tool helps to segment lipid droplets marked with BODIPY. You can find some example images here:

Getting started

To install the tool, drag the link MRI_Lipid_Droplets_Tool.ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the "MRI_Lipid_Droplets_Tool" toolset from the >> button of the ImageJ launcher.

the lipid droplets toolset

  • the first button (the one with the image) opens this help page
  • the s button runs the segmentation on the current image


Open the options-dialog by right-clicking on the s-button:

options of the lipid droplets tool

  • min. size: objects smaller than min. size will be be considered as artefacts of the segmentation and will be removed from the result


result image of lipid droplets tool


A bandpass filter is applied to the input image by using a Gaussian filter and then scaling the image down and up again with increasing scale and taking the difference between the two low-pass filtered images. On the result an automatic threshold (percentile method) is applied. Holes in the objects are filled. An auto-threshold (triangle) is applied to the input image and the resulting mask is used to remove artefacts from the mask of the droplets image. Objects smaller then a give size are removed and a binary watershed transform is used to separate touching droplets. Objects touching the border of the image are removed.

Publications using this tool

  1. Ali, U., Wabitsch, M., Tews, D., and Colitti, M. (2023). Effects of allicin on human Simpson-Golabi-Behmel syndrome cells in mediating browning phenotype. Front. Endocrinol. 14, 1141303. 10.3389/fendo.2023.1141303.
  2. Hammel, J.H., and Bellas, E. (2020). Endothelial cell crosstalk improves browning but hinders white adipocyte maturation in 3D engineered adipose tissue. Integrative Biology 12, 81–89.
  3. Montanari, T., Boschi, F., and Colitti, M. (2019). Comparison of the Effects of Browning-Inducing Capsaicin on Two Murine Adipocyte Models. Front. Physiol. 10, 1380.
  4. Colitti, M., Boschi, F., and Montanari, T. (2018). Dynamic of lipid droplets and gene expression in response to β-aminoisobutyric acid treatment on 3T3-L1 cells". European Journal of Histochemistry 62.
  5. Montanari, T., and Colitti, M. (2018). Simpson–Golabi–Behmel syndrome human adipocytes reveal a changing phenotype throughout differentiation. Histochemistry and Cell Biology, 149, 593–605.

Snap-8242 SGBS BDNF10 40x.jpg - lipid droplets image 1 (196 KB) Volker Baecker, 05/17/2017 11:54 AM

Snap-8235 SGBS BDNF5 40x.jpg - lipid droplets image 2 (255 KB) Volker Baecker, 05/17/2017 11:54 AM

Snap-8224 SGGS BDNF1 40x.jpg - lipid droplets image 3 (176 KB) Volker Baecker, 05/17/2017 11:54 AM

lipid-droplets-toolset.png - the lipid droplets toolset (842 Bytes) Volker Baecker, 05/17/2017 12:02 PM

Options.png - options of the lipid droplets tool (4.59 KB) Volker Baecker, 05/17/2017 01:57 PM

RES01.png - result image of lipid droplets tool (648 KB) Volker Baecker, 05/17/2017 03:19 PM