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.
