Software for processing, quantitative analysis, and visualization of LA-ICP-TOF-MS imaging data
AutoSpect is a software suite for the processing, analysis, visualization, and quantitative interpretation of mass spectrometry imaging data, with a focus on laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS).
The suite includes InSpect, an interactive graphical interface for viewing and analyzing imaging data, together with tools for spectral processing, calibration, quantitative analysis, and spatial data interpretation.
For citation information, see the Citation section.
Current compiled distribution: Windows 64-bit
Required MATLAB Runtime: MATLAB Runtime 9.2 (R2017a), 64-bit
Required Runtime Update: MathWorks R2017a MATLAB Runtime Update
- Overview
- Installation
- Software Licensing
- System Requirements
- Files in a Typical Release
- MATLAB Runtime Notes for Developers
- Troubleshooting
- Updates
- Citation
- Support and Feedback
- About
- MATLAB Runtime
AutoSpect was developed to provide an integrated workflow for working with large, multichannel LA-ICP-TOF-MS imaging datasets. Depending on the installed version and software license, available capabilities may include:
- Interactive inspection and visualization of elemental and isotopic images
- Signal drift correction
- Spectral fitting and peak deconvolution
- Mass calibration
- Concentration calibration
- Quantitative image analysis
- Region-of-interest (ROI) analysis
- Image registration
- Map visualization and comparison
- Export of processed data and quantitative results
The primary user interface for the suite is InSpect.
Download the latest software package from the Releases section of this GitHub repository.
Extract the downloaded archive to a local folder before running the application.
The compiled version of InSpect requires both:
- MATLAB Runtime 9.2 (R2017a), 64-bit
- The separate R2017a MATLAB Runtime Update provided by MathWorks
A licensed installation of MATLAB is not required to run the compiled application. End users also do not need to install MATLAB Compiler.
Go to the MathWorks MATLAB Runtime download page:
https://www.mathworks.com/products/compiler/matlab-runtime.html
On the MathWorks page, locate the row:
R2017a (9.2)
For Windows, complete both of the following steps in this order:
- In the R2017a (9.2) row, select the 64-bit Windows download.
- Download and run the MATLAB Runtime installer.
- Complete the installation.
After the base MATLAB Runtime has been installed:
- Return to the R2017a (9.2) row on the MathWorks MATLAB Runtime page.
- Select Update in the Windows column.
- Download the R2017a Runtime Update.
- Run the update installer and complete the installation.
Important: Install the base R2017a MATLAB Runtime first, and then install the R2017a Runtime Update. Both are required for the AutoSpect/InSpect R2017a distribution.
Administrator privileges may be required depending on the MATLAB Runtime installation location and the security configuration of the computer.
After installing both MATLAB Runtime R2017a and the R2017a Runtime Update:
-
Open the extracted AutoSpect software folder.
-
Run:
InSpect.exe -
Allow the application to initialize. The first launch may take longer while MATLAB Runtime components are loaded.
AutoSpect/InSpect uses a software licensing system. A valid license is required to use licensed functionality, and access to individual capabilities may depend on the privileges enabled for the issued license.
Licensed capabilities may include:
- InSpect — visual inspection and analysis
- Drift Correction
- Spectral Fitting
- Mass / Concentration Calibration
- Quantitative Analysis
- Module — Registration
- Module — Map Viewer
To request a license:
-
Install MATLAB Runtime 9.2 (R2017a), 64-bit and the R2017a Runtime Update, then launch
InSpect.exe. -
If a valid license is not detected, use the license prompt in InSpect to create a license request.
-
Save the license request file generated by InSpect.
-
Create an email with the subject:
InSpect License Request
-
Send the email to both of the following addresses:
- Dr. Andrew M. Crawford:
drcrawford.sci@gmail.com - Michigan State University:
crawf472@msu.edu
- Dr. Andrew M. Crawford:
-
Attach the license request file generated by InSpect to the email.
The license request file contains the information required to generate a license for the computer on which InSpect will be used. A license cannot be issued without the generated request file.
Once the request has been reviewed, the corresponding license file and any necessary installation instructions will be provided by email.
Important: Generate the license request on the computer where InSpect will be used. Licenses may be associated with that computer and may not function if moved to another system.
The currently distributed compiled application is intended for:
- Microsoft Windows, 64-bit
- MATLAB Runtime 9.2 (R2017a), 64-bit
- MathWorks R2017a MATLAB Runtime Update
Hardware requirements depend strongly on dataset size. Large hyperspectral imaging datasets may benefit from substantial system memory and multicore processors.
A release package may contain:
InSpect.exe
README.md
[additional AutoSpect support files]
The MATLAB Runtime installer may be distributed separately rather than included in the AutoSpect release archive.
If an MCRInstaller.exe or MATLAB Runtime installer is included with a release, it may be used instead of downloading the corresponding base runtime directly from MathWorks. The R2017a Runtime Update must still be installed unless it is explicitly included and identified as already applied in the distribution instructions.
AutoSpect/InSpect is compiled using MATLAB Compiler.
For builds produced with MATLAB R2017a, the corresponding runtime is MATLAB Runtime 9.2. The AutoSpect/InSpect R2017a distribution also requires the separate R2017a MATLAB Runtime Update supplied by MathWorks.
From within MATLAB R2017a, the location and version information for the corresponding MATLAB Runtime installer can be displayed with:
mcrinstallerThe runtime bundled with or distributed for a compiled application should correspond to the MATLAB release used to build the application.
Additional MATLAB Compiler deployment documentation is available from MathWorks:
https://www.mathworks.com/help/compiler/
Confirm that both of the following are installed:
- MATLAB Runtime R2017a (9.2), 64-bit
- The R2017a MATLAB Runtime Update
Installing a newer MATLAB Runtime release does not replace the requirement for the R2017a runtime associated with the compiled application. If the base R2017a runtime is installed but the update has not been applied, install the Update shown next to R2017a (9.2) on the MathWorks MATLAB Runtime download page.
Because InSpect is distributed as a downloaded executable, Microsoft Defender SmartScreen may display a warning when InSpect is launched, particularly the first time it is run. This is common for downloaded applications that Windows does not yet recognize.
If you downloaded InSpect from the official AutoSpect distribution source and Windows displays a “Windows protected your PC” message:
- Select More info.
- Confirm that the application shown is
InSpect.exe. - Select Run anyway.
Only bypass the warning if you obtained the software from the official AutoSpect distribution source and are confident that the downloaded files have not been modified.
If Run anyway is not available, the computer may be subject to additional Windows security settings, Microsoft Smart App Control, or organizational IT policies. In that case, contact your system administrator rather than disabling system-wide security protections.
Use the license-request workflow presented by InSpect to generate a license request file. Attach that file to an email sent to drcrawford.sci@gmail.com and crawf472@msu.edu with the subject InSpect License Request.
Performance depends on dataset dimensions, number of measured mass channels, available memory, processor performance, and the analysis being performed. Closing unnecessary applications may make additional system memory available.
New releases, bug fixes, and feature updates are distributed through this repository.
For reproducible analysis, record the AutoSpect/InSpect version used to process data and retain that information with the corresponding analysis records.
If AutoSpect/InSpect is used in work that contributes to a publication, presentation, or other scholarly product, please cite the AutoSpect software paper:
Crawford, A. M.; Zee, D. Z.; Jin, Q.; Sue, A.; Sinha, N.; Ahn, S. H.; O'Halloran, T. V.; MacRenaris, K. W. AutoSpect: an all-in-one software solution for automated processing of LA-ICP-TOF-MS datasets. Journal of Analytical Atomic Spectrometry 2025, 40, 2162–2178.
https://doi.org/10.1039/D5JA00145E
DOI: 10.1039/D5JA00145E
Publisher page:
https://pubs.rsc.org/en/content/articlelanding/2025/ja/d5ja00145e
When reporting analyses performed with AutoSpect/InSpect, we also recommend recording the software version used so that the computational workflow can be reproduced as accurately as possible.
Bug reports, feature requests, and reproducible examples are valuable for continued development.
When reporting a problem, please include, when possible:
- AutoSpect/InSpect version
- Windows version
- Description of the problem
- Steps required to reproduce the problem
- Relevant error messages or screenshots
Do not publicly post software license files, license-request files containing machine-identifying information, private datasets, or other sensitive information in a GitHub issue.
AutoSpect is developed for advanced mass spectrometry imaging data analysis, with an emphasis on making complex LA-ICP-TOF-MS workflows accessible through an integrated graphical environment. For citation information, see the Citation section.
Developer: Andrew M. Crawford, Ph.D.
Michigan State University
MATLAB and MATLAB Runtime are products of The MathWorks, Inc.
MATLAB Runtime allows compiled MATLAB applications to run on supported systems without requiring a licensed MATLAB installation.
For official MATLAB Runtime installation instructions, see:
https://www.mathworks.com/help/compiler/install-the-matlab-runtime.html