Fast and automated processing of multi-channel 3D confocal microscopy data in Fiji[1]:
- 3D datasets are z-projected per channel
- create ROIs of full cells and nuclei based on two channels, e.g. DAPI and actin
- measure the intensity in and area of the ROI for each channel
The pipeline is compatible with standard microscopy data formats working with the Bio-Formats importer[2] of Fiji.
- install Fiji v1.54f or higher according to the documentation
- in Fiji navigate to Plugins → Macros → run
- insert settings and parameters
- choose a random file from a folder to batch process
Give the analysis a try with the file in the testdata folder.
Claudia Catapano, Marina Dietz
[1] Schindelin, J., Arganda-Carreras, I., Frise, E. et al. Nat. Methods 9, 676–682 (2012).
[2] Linkert, M., Rueden, C. T., Allan, C., et al. J. Cell Biol., 189(5), 777–782 (2010).
Please cite our paper when using SingleCellImageQuant for your research.
Catapano, C., Dietz, M.S., Heilemann, M. manuscript in prep.