WiSoft Athena is an image analysis program for easy and rapid assessment of cell biology experimental data. At the touch of a button, it performs ordinary and sophisticated cell biology applications.


An analysis platform for the most common cell biology applications

Superior image analysis with WiSoft Athena

WiSoft Athena is a push-button automated images analysis software for the most common cell biology assays. Image Credit: IDEA Bio-Medical Ltd.

WiScan Athena is a software solution for application-derived image-based experiment analysis and visualization.

Based on sophisticated cell quantification methods for detecting fluorescence intensity and morphological traits, the software includes embedded analytic algorithms, statistical assessment tools, and sub-population analysis tools.

It comprises a library of pre-built analysis modules that can be applied to data sets containing both labeled and non-labeled cells, allowing Athena to analyze pictures captured using both bright field and fluorescent illumination microscopy.

Easy to use, push-button operation

Users of all levels can easily be trained and use this platform independently. Athena provides a library of ready-to-use apps that can be loaded with the single press of a button and enable the user to begin analyzing in minutes following minor parameter calibrations.

The user interface and user experience are tailored for studying image-based cell biology research. With Athena’s pre-configured templates for the most typical cell biology applications, newcomers to high content picture analysis can get started straight away.

Analysis can be performed on a cell-by-cell basis and at population level

For both single cell and subpopulation analyses, individual cells can be examined and quantified. Athena has a population tool that may be used to identify sub-populations of cells in each well and measure attributes of these sub-populations based on cellular phenotypes, similar to cytometry experiments.

Image acquisition and image analysis can be done simultaneously, independently and at separate locations.

It is easy to view and analyze data from any computer by installing Athena software, thereby freeing up the Hermes imager for others to use.

Images captured in the Hermes system are uploaded in real-time to a shared storage, from which Athena software collects data for analysis simultaneously with the picture collecting process, reducing experiment time dramatically. Filters, goals, plate type, fields and coverage, time points, z-stack, and exposure metadata are all saved in the database for future reference.

Straightforward, simple visual results display

The Athena software includes a number of visualization tools for displaying the findings of the study. The user can rapidly and effectively construct a summary report detailing the analysis parameters and showing the findings at the conclusion of each analysis procedure. If necessary, raw data can be effortlessly exported as an excel file to other sources.

Application library

Basic applications

Table 1. Source: IDEA Bio-Medical Ltd.

Application Name Description Color Channels Biological Assays Metrics Quantified
Cell Count Count fluorescently labeled cells or objects 1 Color Nucleus Autophagy; Apoptosis; Cytotoxicity; Cell Viability; Cellular proliferation; Growth rate; Viral plaque assay Area; Fluorescence intensity
Cell Morphology Fluorescently labeled cells or objects shape quantification Ideal for assessment of cellular heath 1 Color Cytoplasm Sub-cellular features quantification: Nuclei; Actin; Microtubules; Golgi; Vesicles; Focal adhesions; Mitochondria Area Perimeter. Shape metrics: Long/short axis length; Elongation ratio; Convex Hull (CH) area; Solidity
Protein Expression Single-cell fluorescence intensity quantification 3 Colors Nucleus Cytoplasm Protein of interest Cell Health assessment; Protein degradation; Protein Localization; Protein translocation; Intracellular distribution analysis; Autophagy (t1/2) assays; Ubiquitination; Protein Aggregation & Accumulation; Transfection efficiency; Gene therapy; Pharmacology & pharmaco-kinetics Area; Perimeter Fluorescence intensity
Cell Cycle Determine cell cycle populations using quantitative DNA labeling 1 Color Nucleus Proliferation assays; Cell cycle arrest detection; Cytotoxicity; Cell Viability Area; Fluorescence intensity
Translocation Quantifies the intensity ratio between the sub-cellular compartments 3 Colors Nucleus Cytoplasm Protein of interest Nuclear signaling assays; Innate immune response; Intra-organelle localization; Intracellular distribution analysis Fluorescence intensity; Nucleus/Cytoplasm Intensity ratio


Specialized applications

Table 2. Source: IDEA Bio-Medical Ltd.

Application Name Description Color Channels Biological Assays Metrics Quantified
Intracellular Granules Quantify cytoplasmic granules for shape, intensity and number 3 Colors Nucleus Cytoplasm Granule channel” Protein aggregation; Vesicle trafficking; Puncta analysis; Endo/exocytosis; Receptor or protein clustering Granule count; Granule intensity; Granule area & shape
Cell Count in Colonies Colony count estimation extrapolated from single cell fluorescence intensities 1 Color Nucleus or cell Bacterial colony cell count; Small, high density cellular colonies e.g. Embryonic stem cells Populations: Single cells, Colonies; Morphology; Fluorescence intensity
Intranuclear Foci Detection and quantification of intranuclear foci and puncta 3 Colors Nucleus Cytoplasm Foci channel Intranuclear protein aggregation; Nucleolar detection; Transcription factor detection; Chromatin detection Nuclear area; Foci count; Foci intensity; Foci area & shape
Quantitative Cytometry Multiplex quantitation of biomarkers or objects within cells or nuclei 1-7 Colors Nucleus or cell 1 color for each object of interest Cytotoxicity; Autophagy; Apoptosis; Cellular fusion; Multi-plasmid transfection; Live/Dead measurement; Bacterial viability; Multi-color foci/puncta Count per object; Intensity per object
Live-Dead Toxicology Quantify live vs. dead cells using cell viability markers 2 Colors Live cells Dead cells Cytotoxicity; Toxicology; Cell viability; Pharmacology & pharmacokinetics Live cells count; Dead cell count
Spheroid Morphology Morphology and fluorescence intensity quantification for 3D cell culture 1 Color Nuclei or Brightfield Drug dose response curves; Cytotoxcitity; Toxicology; Growth curves; Pharmacology & pharmacokinetics Area; Perimeter; Morphology; Solidity; Fluorescence intensity
Colony Detection Label-free cell colony detection providing true single-cell count per colony Brightfield Clonogenic assay; Radiotherapy assay; Dose response curve; Cell viability & proliferation; Pharmacology & pharmacokinetics Colony metrics: Single cell counting; Size; Morphology
Yeast Quantification Brightfield yeast cell segmentation & counting Brightfield + luorescence Cell replication & proliferation; Genetic profiling; RNA colocalization with intracellular organelle in yeast Count close distance events; Number of RNA spots per cell; Number of organelle per cell
Fiber Detection Detect fiber and cytoskeletal intra-cellular structure 1 Color Fibers Cytoskeletal rearrangement Fiber length Count per cell; Fluorescence intensity
Confluency Label-free measure of the area fraction covered by cells or colonies Brightfield Cell viability & proliferation; Radiotherapy assay; Growth rates; Population pharmacology & pharmacokinetics Confluency; Total cell area
Mitochondria Quantification Quantification of mitochondria distribution, morphology and intensity 3 Colors Nucleus Cytoplasm Mitochondria Cellular metabolism; Cell health and viability; Mitochondrial dynamics: Number; Size; Distribution Mitochondria count per cell; Intensity of mitochondria; Morphological properties; Distance from nucleus
Colocalization Measure distance between fluorescence objects 2 Colors Protein-protein interactions; Intracellular transport; Endo/exocytosis; Subcellular drug sequestration Colocalization pixel count; Colocalizing area
Colocalization Measure distance between fluorescence objects 2 Colors Protein-protein interactions; Intracellular transport; Endo/exocytosis; Subcellular drug sequestration Colocalization pixel count; Colocalizing area
Cell Count in Brightfield Label-free cell counting in adherent cell culture Brightfield Cell viability & proliferation; Radiotherapy assay; Growth rates; Pharmacology & pharmacokinetics Count Cell area
Zebrafish Detect fluorescent structures or objects within zebrafish 2 Colors Brightfield Fluorescent object Bacterial infection; Metastasis growth assay  
C. elegans Detect fluorescent structures or objects within C. elegans 2 Colors Brightfield Fluorescent object Cell type identification  
Scratch Assay Detect scratch edge to measure the scratch area relative to total “2 Colors Brightfield Fluorescent object “Wound healing scratch assay  



  • Results report produced in PDF format
  • Windows 7 or Windows is 10 required
  • Raw data can be exported in CSV format to Excel
  • Athena Software runs under 32-bit and 64-bit operating systems


Size and storage options are typical.

Size of typical sample

  • Analyzed data — CSV files — 1–10 KB
  • Images — TIF format 1–10 GB
  • Masks — special format — 1 MB

Storage of typical sample

  • Images in well folders
  • Data set including reports