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MSiReader

MSI Software Solutions, LLC has developed the MSiReader software, a vendor-neutral and user-centric Mass Spectrometry Imaging solution, providing a diverse array of basic and advanced analysis tools. MSiReader enables researchers to turn raw MSI data into biological insights, helping accelerate innovations that positively impact human health.

The vendor-neutral open-source MSiReader, continuously developed and maintained since 2012, has consistently provided advanced MSI analysis functionality, and is widely used across the MSI community.

MSiReader Pro incorporates all the existing analysis functionality, with the addition of intuitive UIs, improved computational efficiency and usability, new and improved analysis tools and visualizations, as well as dedicated professional support.

Contact us today for details, or to request a free demo session.

Looking for a custom solution to further enhance your MSiReader Pro experience? Contact us today for details and pricing.

Features & Functionality

(The 15-Day Free Trial Includes the Full-Functionality of Professional & BioPharma)

Function

Load Single, Multiple or Folder of imzML Files
Customizable Preferences by End-User
Abundance Threshold Filtering
Injection Time Scaling
Single Pixel Selection Tool – View/Export Mass Spectrum
Export High Resolution Heatmaps for Publication in Several File Formats
CVD Compliant Colormap Cividisblack
Free Program Updates (Bug Fixes, Feature Improvements)
Comprehensive User Manual
Interactive Abundance Heatmap m/z Tolerance Update
Interactive Abundance Heatmap Min/Max Value Update
Installation Support
Loading of ThermoFisher *.raw Files
Loading of Arbitrary ROI, nested ROI, and Bespoke Patterns
Custom MSiReader File Formats to Save Data for Session Revisit with Fast Reloading
Abundance Heatmap Normalization
Abundance Hotspot Removal
Colormap Selection (including CVD-compliant colormaps) with Scaling Options
Interpolation of Imaging Data
Sequential Paired Covariance Visualization Tool
Mass Correction including Batch Processing
Centroid Data (Parabolic, MS Peaks or Local Maximum), Peak Exclusion Filter, Abundance Threshold, and Batch Processing
Scan Scrubber (Remove a User-Defined ROI)
Ion Classification Tool for Determining On-Tissue / Background Ions (full integration Q3 of 2023)
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance, and Spectra Above Threshold)
MSi Slicer (Line plot of abundance versus location)
Co-localization and Image Overlay with Transparency
RGB Colocalization
3D Plotting / Visualization
Custom Heatmap Normalization
QA/QC: Mass Measurement Accuracy
QA/QC: Spectral Accuracy
QA/QC: Summary Statistics
ROI Selectors (pixel, line, polygon)
Build, Import and/or Search Custom DB for Annotations
Molecular Formula Adduct Search
SSIM Colocalization Tool Based on Human Perception
Batch Export of Images
MSi Spectrum (Export of Mass Spectra)
MSi Export (Exports m/z and Abundance Data)
MSi Peakfinder (Relative Quantification)
QMSI (Absolute Quantification using Spatial Calibration Curve)
Functional MSI (Percent Isotope Enrichment)
Statistical Analysis (PCA, t-SNE)
Log File Generation
Full Technical Support
Access to New Tools / Features / Workflows Upon Release
BioPharma-Specific Settings (e.g., shots-per-well)
BioPharma: Tools for High-Throughput Screening (HTS) and High Content Screening (HCS)
Plate Location File Generator (to load imzML file format with multiple shots per well)
Ion Abundance Plots (Product, Starting Material, Internal Standard, TIC)
Support for Different Plate Types (6, 24, 96, 384, 1536, 6144 and Custom)
MS Navigation for Product, Starting Material, Internal Standard
Mass Spectrum View with One-Click to View Product, Starting Material or Product Ion
Calculation of Percent Conversion for HTS Applications
Display a Stacked-plot of Abundances per well/shot (TIC, IS, SM, PR)
Display either All Plates, a Unified (merged) View, or a Specific Replicate for a Plate

Basic

Free

Load Single, Multiple or Folder of imzML Files
✓
Customizable Preferences by End-User
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Export High Resolution Heatmaps for Publication in Several File Formats
✓
CVD Compliant Colormap Cividisblack
✓
Free Program Updates (Bug Fixes, Feature Improvements)
✓
Comprehensive User Manual
✓
Interactive Abundance Heatmap m/z Tolerance Update
✓
Interactive Abundance Heatmap Min/Max Value Update
✓
Installation Support
✓
Loading of ThermoFisher *.raw Files
Loading of Arbitrary ROI, nested ROI, and Bespoke Patterns
Custom MSiReader File Formats to Save Data for Session Revisit with Fast Reloading
Abundance Heatmap Normalization
Abundance Hotspot Removal
Colormap Selection (including CVD-compliant colormaps) with Scaling Options
Interpolation of Imaging Data
Sequential Paired Covariance Visualization Tool
Mass Correction including Batch Processing
Centroid Data (Parabolic, MS Peaks or Local Maximum), Peak Exclusion Filter, Abundance Threshold, and Batch Processing
Scan Scrubber (Remove a User-Defined ROI)
Ion Classification Tool for Determining On-Tissue / Background Ions (full integration Q3 of 2023)
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance, and Spectra Above Threshold)
MSi Slicer (Line plot of abundance versus location)
Co-localization and Image Overlay with Transparency
RGB Colocalization
3D Plotting / Visualization
Custom Heatmap Normalization
QA/QC: Mass Measurement Accuracy
QA/QC: Spectral Accuracy
QA/QC: Summary Statistics
ROI Selectors (pixel, line, polygon)
Build, Import and/or Search Custom DB for Annotations
Molecular Formula Adduct Search
SSIM Colocalization Tool Based on Human Perception
Batch Export of Images
MSi Spectrum (Export of Mass Spectra)
MSi Export (Exports m/z and Abundance Data)
MSi Peakfinder (Relative Quantification)
QMSI (Absolute Quantification using Spatial Calibration Curve)
Functional MSI (Percent Isotope Enrichment)
Statistical Analysis (PCA, t-SNE)
Log File Generation
Full Technical Support
Access to New Tools / Features / Workflows Upon Release
BioPharma-Specific Settings (e.g., shots-per-well)
BioPharma: Tools for High-Throughput Screening (HTS) and High Content Screening (HCS)
Plate Location File Generator (to load imzML file format with multiple shots per well)
Ion Abundance Plots (Product, Starting Material, Internal Standard, TIC)
Support for Different Plate Types (6, 24, 96, 384, 1536, 6144 and Custom)
MS Navigation for Product, Starting Material, Internal Standard
Mass Spectrum View with One-Click to View Product, Starting Material or Product Ion
Calculation of Percent Conversion for HTS Applications
Display a Stacked-plot of Abundances per well/shot (TIC, IS, SM, PR)
Display either All Plates, a Unified (merged) View, or a Specific Replicate for a Plate

Professional

Subscription

Load Single, Multiple or Folder of imzML Files
✓
Customizable Preferences by End-User
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Export High Resolution Heatmaps for Publication in Several File Formats
✓
CVD Compliant Colormap Cividisblack
✓
Free Program Updates (Bug Fixes, Feature Improvements)
✓
Comprehensive User Manual
✓
Interactive Abundance Heatmap m/z Tolerance Update
✓
Interactive Abundance Heatmap Min/Max Value Update
✓
Installation Support
✓
Loading of ThermoFisher *.raw Files
✓
Loading of Arbitrary ROI, nested ROI, and Bespoke Patterns
✓
Custom MSiReader File Formats to Save Data for Session Revisit with Fast Reloading
✓
Abundance Heatmap Normalization
✓
Abundance Hotspot Removal
✓
Colormap Selection (including CVD-compliant colormaps) with Scaling Options
✓
Interpolation of Imaging Data
✓
Sequential Paired Covariance Visualization Tool
✓
Mass Correction including Batch Processing
✓
Centroid Data (Parabolic, MS Peaks or Local Maximum), Peak Exclusion Filter, Abundance Threshold, and Batch Processing
✓
Scan Scrubber (Remove a User-Defined ROI)
✓
Ion Classification Tool for Determining On-Tissue / Background Ions (full integration Q3 of 2023)
✓
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance, and Spectra Above Threshold)
✓
MSi Slicer (Line plot of abundance versus location)
✓
Co-localization and Image Overlay with Transparency
✓
RGB Colocalization
✓
3D Plotting / Visualization
✓
Custom Heatmap Normalization
✓
QA/QC: Mass Measurement Accuracy
✓
QA/QC: Spectral Accuracy
✓
QA/QC: Summary Statistics
✓
ROI Selectors (pixel, line, polygon)
✓
Build, Import and/or Search Custom DB for Annotations
✓
Molecular Formula Adduct Search
✓
SSIM Colocalization Tool Based on Human Perception
✓
Batch Export of Images
✓
MSi Spectrum (Export of Mass Spectra)
✓
MSi Export (Exports m/z and Abundance Data)
✓
MSi Peakfinder (Relative Quantification)
✓
QMSI (Absolute Quantification using Spatial Calibration Curve)
✓
Functional MSI (Percent Isotope Enrichment)
✓
Statistical Analysis (PCA, t-SNE)
✓
Log File Generation
✓
Full Technical Support
✓
Access to New Tools / Features / Workflows Upon Release
✓
BioPharma-Specific Settings (e.g., shots-per-well)
BioPharma: Tools for High-Throughput Screening (HTS) and High Content Screening (HCS)
Plate Location File Generator (to load imzML file format with multiple shots per well)
Ion Abundance Plots (Product, Starting Material, Internal Standard, TIC)
Support for Different Plate Types (6, 24, 96, 384, 1536, 6144 and Custom)
MS Navigation for Product, Starting Material, Internal Standard
Mass Spectrum View with One-Click to View Product, Starting Material or Product Ion
Calculation of Percent Conversion for HTS Applications
Display a Stacked-plot of Abundances per well/shot (TIC, IS, SM, PR)
Display either All Plates, a Unified (merged) View, or a Specific Replicate for a Plate

BioPharma

Subscription

Load Single, Multiple or Folder of imzML Files
✓
Customizable Preferences by End-User
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Export High Resolution Heatmaps for Publication in Several File Formats
✓
CVD Compliant Colormap Cividisblack
✓
Free Program Updates (Bug Fixes, Feature Improvements)
✓
Comprehensive User Manual
✓
Interactive Abundance Heatmap m/z Tolerance Update
✓
Interactive Abundance Heatmap Min/Max Value Update
✓
Installation Support
✓
Loading of ThermoFisher *.raw Files
✓
Loading of Arbitrary ROI, nested ROI, and Bespoke Patterns
✓
Custom MSiReader File Formats to Save Data for Session Revisit with Fast Reloading
✓
Abundance Heatmap Normalization
✓
Abundance Hotspot Removal
✓
Colormap Selection (including CVD-compliant colormaps) with Scaling Options
✓
Interpolation of Imaging Data
✓
Sequential Paired Covariance Visualization Tool
✓
Mass Correction including Batch Processing
✓
Centroid Data (Parabolic, MS Peaks or Local Maximum), Peak Exclusion Filter, Abundance Threshold, and Batch Processing
✓
Scan Scrubber (Remove a User-Defined ROI)
✓
Ion Classification Tool for Determining On-Tissue / Background Ions (full integration Q3 of 2023)
✓
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance, and Spectra Above Threshold)
✓
MSi Slicer (Line plot of abundance versus location)
✓
Co-localization and Image Overlay with Transparency
✓
RGB Colocalization
✓
3D Plotting / Visualization
✓
Custom Heatmap Normalization
✓
QA/QC: Mass Measurement Accuracy
✓
QA/QC: Spectral Accuracy
✓
QA/QC: Summary Statistics
✓
ROI Selectors (pixel, line, polygon)
✓
Build, Import and/or Search Custom DB for Annotations
✓
Molecular Formula Adduct Search
✓
SSIM Colocalization Tool Based on Human Perception
✓
Batch Export of Images
✓
MSi Spectrum (Export of Mass Spectra)
✓
MSi Export (Exports m/z and Abundance Data)
✓
MSi Peakfinder (Relative Quantification)
✓
QMSI (Absolute Quantification using Spatial Calibration Curve)
✓
Functional MSI (Percent Isotope Enrichment)
✓
Statistical Analysis (PCA, t-SNE)
✓
Log File Generation
✓
Full Technical Support
✓
Access to New Tools / Features / Workflows Upon Release
✓
BioPharma-Specific Settings (e.g., shots-per-well)
✓
BioPharma: Tools for High-Throughput Screening (HTS) and High Content Screening (HCS)
✓
Plate Location File Generator (to load imzML file format with multiple shots per well)
✓
Ion Abundance Plots (Product, Starting Material, Internal Standard, TIC)
✓
Support for Different Plate Types (6, 24, 96, 384, 1536, 6144 and Custom)
✓
MS Navigation for Product, Starting Material, Internal Standard
✓
Mass Spectrum View with One-Click to View Product, Starting Material or Product Ion
✓
Calculation of Percent Conversion for HTS Applications
✓
Display a Stacked-plot of Abundances per well/shot (TIC, IS, SM, PR)
✓
Display either All Plates, a Unified (merged) View, or a Specific Replicate for a Plate
✓

*The ‘Download’ button above provides a fully-functional 15-Day FREE Trial,
which includes access to all Professional & BioPharma features.
After 15 days, you will still have access to the Basic version and features.

Compare Plans

MSiReader

The vendor-neutral open-source MSiReader, continuously developed and maintained since 2012, has consistently provided advanced MSI analysis functionality, and is widely used across the MSI community.

MSiReader Pro incorporates all the existing analysis functionality, with the addition of intuitive UIs, improved computational efficiency and usability, new and improved analysis tools and visualizations, as well as dedicated professional support.

Contact us today for details, or to request a free demo session.

Looking for a custom solution to further enhance your MSiReader Pro experience? Contact us today for details and pricing.

Features & Functionality

(The 15-Day Free Trial Includes the Full-Functionality of Professional & BioPharma)

*The ‘Download’ button above provides a fully-functional 15-Day FREE Trial, which includes access to all Professional & BioPharma features. After 15 days, you will still have access to the Basic version and features.

Product License Agreement

*The ‘Download’ button above provides a fully-functional 15-Day FREE Trial,
which includes access to all Professional & BioPharma features.
After 15 days, you will still have access to the Basic version and features.