Table 4.
Image analysis softwares, commercially available and open sources, for multiplexed staining.
| Company | Software package | Modules | Data visualisation | Availability |
|---|---|---|---|---|
| Akoya Biosciences | InForm/Phenopther Packet | Colour-Based Co-localisation, Tissue Segmentation, Cell/Object Segmentation, Cell Phenotyping, Scoring and Automated Quantitation using Batch Analysis |
Density Raw Data Spatial plots, Bar graphics, Head maps |
Licensed |
| CompuCyte | iCyte/iBroser/iNovator | Nucleus Segmentation or Phantom Contouring, Measures Associated Signals | Density Raw Data | Licensed |
| HistoRx | AQUAnalysis | Signal Intensity Quantification Per Unit Area and Per Layer | Density Raw Data | Licensed |
| Indica Labs | HALO | Area Quantification, Co-localisation, Immune Cell Proximity, Spatial Analysis, Tissue Classifier | Density Raw Data, Percentage, H-score, Spatial Plot, Histogram | Licensed |
| Leica Biosystems | Aperio ImageScope | Pixel-Based Analysis, Cellular identification, Area Quantification and Positive Pixel Count IF Algorithm | Density Raw Data | Licensed |
| Media Cybernetics | Image-Pro | Colour-Based, Nuclear segmentation, Cell quantification, Macro-enabled Advanced Image Processing Solution | Density Raw Data | Licensed |
| NeoGenomics | MultiOmyx Quantification Programme | Epithelial tissue reconstruction, Cellular and Subcellular Segmentation, Cell Phenotyping, Quantification Algorithms | Density Raw Data | Licensed |
| NIH | Image J | Colour-Based, User Interactive Segmentation | Histograms and Profile Plots | Open |
| SlidePath | SlidePath’s Tissue Image Analysis | Membrane, Nuclear and Positive Pixel Quantification | Density Raw Data | Licensed |
| TissueGnostics | HistoQuest/TissueQuest/StrataQuest | Nuclei-Based Segmentation of Tissues, Cell Phenotyping | Density Raw Data | Licensed |
| Visiopharm | Visimoph Tissuemorph | Signal Intensity, Area, Counting Objects, Spatial Analysis, Clustering Statistical Analysis, Batch Analysis and Algorithm Creator. | Density Raw Data, Phenotypic Matrix, t-SNE Plots | Licensed |
| Miltenyi Biotec | Qi Tissue™ Image Analysis Software | Cell segmentation algorithms, Flexible gating and clustering cell phenotypes | Density Raw Data, Ploting tools as t-SNE and UMAP plots, distance mapping clustering and other visualisation tools such as heatmaps, scatter and histogram plots | Licensed |
| https://qupath.github.io | QuPath/CytoMap | View Measurements in Context by Colour Coding Objects According to Their Features, Flexible Object Classification, Trainable Cell Classification and Quantification | Density Raw Data, t-SNE plots, distance mapping clustering and other visualisation tools such as heatmaps, scatter and histogram plots | Open |
| https://cellprofiler.org/ | Cell Profiler/Cell Analyst | Based and Colour Object Identification, Size, Shape, Colour Intensity, Texture, and Number Neighbour Quantification. | Density Plot, Histogram | Open |