| layout | title | permalink |
|---|---|---|
page |
Single Cell Imaging Software |
/software_singlecell/ |
| Software Information | Functionality | |||||||
| Name | Purpose | Language | Store | Viz | Norm | Seg | Ptype | Spatial |
| VectraPolarisData | Example mIF datasets | R (Bioc) | ✓ | |||||
| histoCAT | Computational histology topography cytometry analysis toolbox | MATLAB, GUI | ✓ | ✓ | ✓ | |||
| Squidpy | Tool for the analysis and visualization of spatial molecular data | Python | ✓ | ✓ | ✓ | |||
| Giotto | Tools to process, analyze and visualize single-cell spatial expression data | R, GUI, Python depends | ✓ | ✓ | ✓ | |||
| imcRTools | Analysis of imaging mass cytometry and other highly multiplexed data | R (Bioc) | ✓ | ✓ | ✓ | |||
| SVCA | Computational framework for the analysis of spatial molecular data | Python, R depends | ✓ | ✓ | ✓ | |||
| SPIAT | Data processing, quality control, visualization, data analysis tools | R | ✓ | |||||
| spatialTIME | Spatial analysis of mIF data | R | ✓ | ✓ | ✓ | |||
| mxnorm | Normalization techniques for mIF data | R, Python depends | ✓ | ✓ | ✓ | ✓ | ||
| Seurat | Toolkit for QC, analysis, and exploration of single-cell omics data | R | ✓ | ✓ | ✓ | |||
| QuPath | Powerful, flexible, extensible platform for bioimage analysis | GUI, Java | ✓ | ✓ | ✓ | ✓ | ✓ | |
| HALO | Platform for quantitative tissue analysis in digital pathology | Closed source, GUI | ✓ | ✓ | ✓ | ✓ | ||
| inForm | Visualizing, segmenting, and phenotyping images from Vectra instruments | Closed source, GUI | ✓ | ✓ | ✓ | |||
| Cytomapper | Visualization of cell-level info obtained by multiplexed imaging cytometry | R (Bioc) | ✓ | |||||
| CyLinter | Quality control software for multiplex microscopy | Python | ✓ | |||||
| CellProfiler | Interactive data analysis for highthroughput, image-based experiments | Python | ✓ | |||||