ImageJ / Fiji can be extended with hundreds of plugins: special-purpose software components that extend ImageJ’s functionality in scientific image processing and analysis.

Here are a few publications which may be helpful:

Biological imaging software tools
Eliceiri KW et al.. Nat. Methods 9, 2012 697–710. doi:10.1038/nmeth.2084

JACoP (Just Another Co-localization Plug-in): A guided tour into subcellular colocalization analysis in light Microscopy
Bolte S, Cordelieres FP. Journal of Microscopy, Vol. 224, Pt 3 December 2006, 213–232. doi.org/10.1111/j.1365-2818.2006.01706.x

A practical guide to evaluating colocalization in biological microscopy
Dunn KW, Kamocka MM, McDonald JH. Am J Physiol Cell Physiol 300: C723–C742, 2011. doi:10.1152/ajpcell.00462.2010.

DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis
Gilles JF, Santos MD, Boudier T, Bolte S, Heck N. Methods 115, 2017, 55–64. doi.org/10.1016/j.ymeth.2016.11.016

TrackMate: An open and extensible platform for single-particle tracking
Tinevez J-Y. et al. Methods 115, 2017, 80–90. doi.org/10.1016/j.ymeth.2016.09.016

DeconvolutionLab2: An open-source software for deconvolution microscopy.
Daniel Sage. Methods 115, 2017, 28–41. doi.org/10.1016/j.ymeth.2016.12.015

MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ
Legland D, Arganda-Carreras I, Andrey P. Bioinformatics, 32(22), 2016, 3532–3534. doi:10.1093/bioinformatics/btw413

Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy
Diel EE, Lichtman JW, Richardson DS. Nature Protocols, 15 September 2020, 2773–2784. doi.org/10.1038/s41596-020-0360-2

PicPreview and PicSummary: Two Timesaving Plugins for the Fluorescence Microscopist.
Vieyres G. Cells 2021, 10, 846. doi.org/10.3390/cells10040846