library

napari-lattice is a napari plugin designed for the analysis and visualization of Lattice Lightsheet Microscopy (LLSM) and Oblique Plane Microscopy (OPM) data, particularly focusing on data acquired from Zeiss Lattice Lightsheet systems. Also available as lls-core - a command line version of the same tool which does not require napari.

napari-lattice allows users to deskew and deconlolve lattice light sheet, or any oblique plane microscopy, data. To speed processing, users can provide ROIs to be cropped and processed separately.  This significantly speeds up processing time and allows many options for parallelisation. 

The Plant Computer Vision (PlantCV) software package, is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. 

PlantCV v2 is the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

PlantCV is composed of modular functions in order to be applicable to a variety of plant types and imaging systems. PlantCV currently supports the analysis of standard RGB color images (aka "VIS"), standard grayscale images (e.g. near-infrared, "NIR"), thermal infrared images, grayscale images from chlorophyll fluorescence imaging systems ("PSII"), and hyperspectral ("ENVI") images. 

AnyLabeling is Effortless AI-assisted data labeling tool with AI support from Segment Anything and YOLO models!

AnyLabeling = LabelImg + Labelme + Improved UI + Auto-labeling

Installation

Standalone (executable)

The executable file links are provided in Assets section here

Install from source

git clone https://github.com/vietanhdev/anylabeling
cd anylabeling
pip install .

Install from PyPI

pip install anylabeling

With GPU support:

pip install anylabeling-gpu

BraiAn is an open-source suite of tools designed to simplify signal quantification, analysis and visualization of large datasets typically obtained in whole-brain imaging experiments, following registration to an atlas. 

The package consists of two separate modules.

1. BrainAnDetect: A QuPath extension for multi-channel cell segmentation across large and variable datasets. It leverages QuPath's built in algorithms for cell detection, and features additional options for refining signal quantification, including machine-learning-based object classification, region-specific cell segmentation, multiple marker co-expression analysis, and an interface for selective exclusion of damaged tissue portions.
2. BraiAnalyse: A modular Python library for the easy navigation, visualization, and analysis of whole-brain quantification outputs.

# 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