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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.

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

Features & Functionality

Function

Export High Resolution Heatmaps for Publication in Several File Formats
Customizable Preferences by End-User
Load Single, Multiple or Entire Folder of Data
File Conversion Tools
Normalization (Reference Peak, TIC, local TIC)
Hotspot Removal
Colormap Selection with Scaling Options (linear, log)
Interpolation of Imaging Data
Sequential Paired Covariance Visualization Tool
Abundance Threshold Filtering
Injection Time Scaling
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance and Spectra Above Threshold)
Save Session to Revisit Study
Single Pixel Selection Tool – View/Export Mass Spectrum
Launch METASPACE for Annotation
Mass Recalibration
Scan Scrubber (Remove a User-Defined ROI)
Centroid Data (Parabolic, MS Peaks or Local Maximum)
MSi Slicer (Line plot of abundance versus location)
Co-localization and Image Overlay with transparency
RGB Colocalization
3D Plotting / Visualization
QA/QC: Summary Statistics
QA/QC: Mass Measurement Accuracy
QA/QC: Spectral Accuracy
Molecular Formula Adduct Search
Build, Import and/or Search Custom DB for Annotations
SSIM Colocalization Tool
MSi Peakfinder (relative quantification)
QMSI (absolute quantification using spatial calibration curve)
Functional MSI (Percent Isotopic Enrichment)
Statistical Analysis (PCA, t-SNE)
Installation Support
Full Technical Support
Free program updates (bug fixes, feature improvements)
Access to new tools/features/workflows regularly added

15-Day Trial

Free

Export High Resolution Heatmaps for Publication in Several File Formats
✓
Customizable Preferences by End-User
✓
Load Single, Multiple or Entire Folder of Data
✓
File Conversion Tools
✓
Normalization (Reference Peak, TIC, local TIC)
✓
Hotspot Removal
✓
Colormap Selection with Scaling Options (linear, log)
✓
Interpolation of Imaging Data
✓
Sequential Paired Covariance Visualization Tool
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance and Spectra Above Threshold)
✓
Save Session to Revisit Study
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Launch METASPACE for Annotation
✓
Mass Recalibration
✓
Scan Scrubber (Remove a User-Defined ROI)
✓
Centroid Data (Parabolic, MS Peaks or Local Maximum)
✓
MSi Slicer (Line plot of abundance versus location)
✓
Co-localization and Image Overlay with transparency
✓
RGB Colocalization
✓
3D Plotting / Visualization
✓
QA/QC: Summary Statistics
✓
QA/QC: Mass Measurement Accuracy
✓
QA/QC: Spectral Accuracy
✓
Molecular Formula Adduct Search
✓
Build, Import and/or Search Custom DB for Annotations
✓
SSIM Colocalization Tool
✓
MSi Peakfinder (relative quantification)
✓
QMSI (absolute quantification using spatial calibration curve)
✓
Functional MSI (Percent Isotopic Enrichment)
✓
Statistical Analysis (PCA, t-SNE)
✓
Installation Support
✓
Full Technical Support
✓
Free program updates (bug fixes, feature improvements)
✓
Access to new tools/features/workflows regularly added
✓

Basic

Free

Export High Resolution Heatmaps for Publication in Several File Formats
✓
Customizable Preferences by End-User
✓
Load Single, Multiple or Entire Folder of Data
✓
File Conversion Tools
✓
Normalization (Reference Peak, TIC, local TIC)
✓
Hotspot Removal
✓
Colormap Selection with Scaling Options (linear, log)
✓
Interpolation of Imaging Data
✓
Sequential Paired Covariance Visualization Tool
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance and Spectra Above Threshold)
✓
Save Session to Revisit Study
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Launch METASPACE for Annotation
✓
Mass Recalibration
Scan Scrubber (Remove a User-Defined ROI)
Centroid Data (Parabolic, MS Peaks or Local Maximum)
MSi Slicer (Line plot of abundance versus location)
Co-localization and Image Overlay with transparency
RGB Colocalization
3D Plotting / Visualization
QA/QC: Summary Statistics
QA/QC: Mass Measurement Accuracy
QA/QC: Spectral Accuracy
Molecular Formula Adduct Search
Build, Import and/or Search Custom DB for Annotations
SSIM Colocalization Tool
MSi Peakfinder (relative quantification)
QMSI (absolute quantification using spatial calibration curve)
Functional MSI (Percent Isotopic Enrichment)
Statistical Analysis (PCA, t-SNE)
Installation Support
✓
Full Technical Support
Free program updates (bug fixes, feature improvements)
✓
Access to new tools/features/workflows regularly added

Professional

Subscription

Export High Resolution Heatmaps for Publication in Several File Formats
✓
Customizable Preferences by End-User
✓
Load Single, Multiple or Entire Folder of Data
✓
File Conversion Tools
✓
Normalization (Reference Peak, TIC, local TIC)
✓
Hotspot Removal
✓
Colormap Selection with Scaling Options (linear, log)
✓
Interpolation of Imaging Data
✓
Sequential Paired Covariance Visualization Tool
✓
Abundance Threshold Filtering
✓
Injection Time Scaling
✓
Visualization Tools (Abundance Rank, TIC, # Analytes, Summed m/z Abundance and Spectra Above Threshold)
✓
Save Session to Revisit Study
✓
Single Pixel Selection Tool – View/Export Mass Spectrum
✓
Launch METASPACE for Annotation
✓
Mass Recalibration
✓
Scan Scrubber (Remove a User-Defined ROI)
✓
Centroid Data (Parabolic, MS Peaks or Local Maximum)
✓
MSi Slicer (Line plot of abundance versus location)
✓
Co-localization and Image Overlay with transparency
✓
RGB Colocalization
✓
3D Plotting / Visualization
✓
QA/QC: Summary Statistics
✓
QA/QC: Mass Measurement Accuracy
✓
QA/QC: Spectral Accuracy
✓
Molecular Formula Adduct Search
✓
Build, Import and/or Search Custom DB for Annotations
✓
SSIM Colocalization Tool
✓
MSi Peakfinder (relative quantification)
✓
QMSI (absolute quantification using spatial calibration curve)
✓
Functional MSI (Percent Isotopic Enrichment)
✓
Statistical Analysis (PCA, t-SNE)
✓
Installation Support
✓
Full Technical Support
✓
Free program updates (bug fixes, feature improvements)
✓
Access to new tools/features/workflows regularly added
✓

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.

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

Features & Functionality

Product License Agreement