Illumination correction

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. 

Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization. Fractal provides distributed workflows that convert TBs of image data into OME-Zarr files. The platform then processes the 3D image data by applying tasks like illumination correction, maximum intensity projection, 3D segmentation using cellpose and measurements using napari workflows. The pyramidal OME-Zarr files enable interactive visualization in the napari viewer.

Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns.

The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.

Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation.

It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching