Semi-automated

Aligning Big Brains & Atlases (ABBA) is a set of software components which allows users to register images of thin serial biological tissue sections, cut in any orientation (coronal, sagittal or horizontal) to atlases, usually brain atlases. ABBA is available as a Fiji plugin for performing registration; a QuPath extension is also available and recommended. Typically, a set of serial sections is defined as a QuPath project, that is registered within Fiji. The registration results can then imported back into QuPath for downstream processing (cell detection and classification, cell counting per region, etc.).

Available atlases include the 3D mouse Allen Brain atlas and the Waxholm Space Atlas of the Sprague Dawley Rat Brain. Depending on your installation method, you may also access all BrainGlobe atlases.

ImageJ macro script to streamline the original NMJ-morph methodology doi:10.1098/rsob.160240
Also requires Binary Connectivity https://blog.bham.ac.uk/intellimic/g-landini-software/ 

Ultralytics creates cutting-edge, state-of-the-art (SOTA) YOLO models built on years of foundational research in computer vision and AI. Constantly updated for performance and flexibility, our models are fast, accurate, and easy to use. They excel at object detection, tracking, instance segmentation, image classification, and pose estimation tasks.

SNT is ImageJ’s framework for tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multidimensional microscopy data, semi-automated and automated routines, and options for editing traces. For data analysis, SNT features advanced visualization tools, access to all major morphology databases, and support for whole-brain circuitry data.

Big-FISH is a python package for the analysis of smFISH images (2D/3D). It includes various methods to analyze microscopy images, such spot detection and segmentation of cells and nuclei.