AssayScope is an intuitive application dedicated to large scale image processing and data analysis. It is meant for histology, cell culture (2D, 3D, 2D+t) and phenotypic analysis.
The Allen Cell Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.
It consists of two complementary elements:
Classic image segmentation workflows for 20 distinct intracellular structure localization patterns. A visual “lookup table” is outlining the modular algorithmic steps for each segmentation workflow. This provides an intuitive guide for selection or construction of new segmentation workflows for a user’s particular segmentation task.
Human-in-the-loop iterative deep learning segmentation workflow trained on ground truth manually curated data from the images segmented with the segmentation workflow. Importantly, this module was not released yet.
DeconvolutionLab2 includes a friendly user interface to run the following deconvolution algortihms: Regularized Inverse Filter, Tikhonov Inverse Filter, Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative Least Squares, Bounded-Variable Least Squares, Van Cittert, Tikhonov-Miller, Iterative Constraint Tikhonov-Miller, FISTA, ISTA.
The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.
"The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes."
