Lipid droplet analysis

Dear All,

I have recently optimized a pipeline for the analyzis of lipid droplets in mammalian cells. In the protocol, cells are stained by DAPI, Bodipy and Phalloidin to visualize the nuclei, the lipid droplets and the cytoplasm, respecively. As I don’t have many experiences in image analysis, I would like to ask your opinion about the enclosed pipeline. Which modules, settings should be changed? Unfortunately one cycle of image analysis (one image set) on my personal computer takes around 4-5 min. Do you have any suggestions to reduce it?



PS: in the attachment you can find an representative image set, the pipeline, a dtabase and properties file.
Test pipeline 0308.rar (3.93 MB)

Hi Gergo,

I’m attaching a revised pipeline that hopefully should get you pointed in the right direction. I’ve removed all the modules other than those having to do with pre-processing and object detection.

One big change was using speckle enhancement to highlight the droplets for detection; however, I’m not familiar with what a droplet should look like, so this is subject to revision.

I think the reason the pipeline was taking so long was that you had unchecked “Speed up by using lower-resolution image to find local maxima.” It is extremely rare to find cases where unchecking this box helps matters; fortunately, I think this case is not one of them :smile:

2012_08_03.cp (12.8 KB)

Hello Mark,

Thank you for your correction. Now the pipeline is working very well. I changed the settings for speckle enhancement to improve the detection of the droplets. With these settings the detection of the individual droplets are better but the area covered by the droplets is somewhat lower. I will compare all the differences accurately.