A novel ImageJ plugin is designed to extend the depth-of-field (DoF) by seamlessly fusing a series of multi-focus images, allowing for in-depth analysis. Moreover, it has been tested on multi-exposure image stacks, demonstrating its adeptness in preserving intricate details within both poorly and brightly illuminated regions of 3-D specimens. The significance of this capability becomes particularly apparent when dealing with images that exhibit a limited DoF and varying exposure settings under low signal-to-noise ratio conditions. The plugin's effectiveness has been thoroughly validated through the processing and analysis of numerous image stacks featuring diverse diatom and cyanobacteria species. The proposed methodology incorporates a two-scale decomposition (TSD) scheme, complemented by the refinement of weight maps using edge-preserving filtering (EPF). This dual approach ensures the preservation of fine details in the fused image while simultaneously minimizing noise. Such innovations make this plugin a valuable tool for researchers and analysts working with complex image datasets.