Software Platforms
There are a number of software options for analysis available but in essence, they all lead to similar workflows. The stained tissue regardless of type, staining protocol or staining complexity, must be annotated into requisite regions of interest based on the research question being asked.
(opens in a new window)Indica Labs HALO provides quantitative and intuitive image analysis for digital pathology. Choose from a broad range of brightfield, fluorescent and multiplex image analysis tools to complement your research.
(opens in a new window)Indica Labs HALO AI is a train-by-example analysis software for digital pathology. The intuitive interface coupled with advanced deep learning networks enable easy tuning and optimisation for segmentation, classification or phenotyping analysis challenges.
(opens in a new window)Aperio Algorithm Toolkit includes machine learning algorithms for nuclear/ membrane/ cytoplasmic detection and deconvolution and co-localisation.
(opens in a new window)Akoya inFORM is an automated image analysis software for multiplexed tissue studies. It supports spectral unmixing, image stitching, and cell segmentation, enabling researchers to quantify biomarker expression and spatial relationships across specimens. Results can be exported for further analysis using compatible tools.
(opens in a new window)Phenoptr Reports offers robust and user-friendly tools for analysing spatial relationships among cellular phenotypes and visualising these relationships overlaid on tissues. Identify cells co-expressing specific markers, assess the quality of an unmixing library, and present the results in easily shareable and comprehensible data reports.
(opens in a new window)QuPath - benefit from our experience with this open-source software for bioimage analysis often used for digital pathology applications. Offers a powerful set of tools for working with whole slide images. Read more: (opens in a new window)Bankhead, P et. al. 2017