2D

MetaXpress or in full name "MetaXpress® High-Content Image Acquisition and Analysis Software" is a commercially available closed source software for high-content analysis from Molecular Devices, LLC.. The program is a kind of visually guided workflow programming environment. There is a programming module called CME (custom module editor) which lets one setup integrated workflows for bioimage analysis with visual feedback. It is designed for high-throughput in connection with a included database which stores the experimental data. 

It has several toolboxes for semiautomated processing of various tasks:

3D Analysis (requires Custom Module Editor), Curve fitting, Transmitted light segmentation (requires Custom Module Editors), Angiogenesis tube formation, Cell cycle, Cell health, Cell scoring , Count nuclei, Granularity, Live/dead , Mitotic index, Micronuclei , Monopole detection, Multi-Wavelength cell scoring, Multi-wavelength translocation, Neurite outgrowth , Transfluor® Assay, Translocation* (includes Translocation-Enhanced*) , Transfluor HT Assay , Nuclear translocation HAT, Cell proliferation HT

After the workflow is setup it is possible to apply it automatically to a stack of stored images. The derived data from those analyses is stored in the metaxpress database and can be exported from there.

The use of each toolbox requires a separate license.

# Install the ultralytics package from PyPI
pip install ultralytics

You can also install ultralytics directly from the Ultralytics GitHub repository. This can be useful if you want the latest development version. Ensure you have the Git command-line tool installed, and then run:

# Install the ultralytics package from GitHub
pip install git+https://github.com/ultralytics/ultralytics.git@main

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.