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IMAGEREVEAL MS - Support
Mass Spectrometry Imaging Data Analysis Software
User’s guide/troubleshooting (PDF files)
1. Introduction
2. Before analysis
2-1 Setting a file location for saving temporary data matrix files (on initial startup only)
2-2 Creating a data matrix
2-2-1 Editing the compound template
3. Analysis
3-1 Find components that differ between regions
3-1-1 Find components that differ between regions -Testing
3-1-2 Find components that differ between regions -PCA
3-1-3 Find components that differ between regions -PLS
3-1-4 Saving the shape of the ROI
3-1-5 ROI settings: adding attributes
3-2 Visualization within a sample section
3-2-1 Investigating localization within a sample section (Similar image extraction)
3-2-2 Image registration
3-2-3 Investigating localization within a sample section (Image classification)
3-2-4 Segmentation
3-2-5 To make false color images by UMAP
3-4 MS images related operations
3-4-1 Superimposing imagestion
3-4-2 Calculations combining multiple images
3-4-3 Settings for copying MS images
3-4-4 Tagging (color coding)
3-4-5 Method to check MS images easily
3-4-6 Adjusting MS images
4. FAQ
4-1 Using the HELP function
4-2 Error message_Reference image targeted for processing
4-3 If statistics such as P-values are not displayed
4-4 If a box plot doesn’t appear
4-5 If you cannot enter a small value when specifying the bin width in non-target analysis
4-6 To use a common color bar for multiple data
4-7 If it is difficult to find the differences between images using differential analysis of multiple data files
4-8 Problems with IMDX files that have been converted from imzML
4-9 If the y-axis scale on the spectrum doesn't look right
4-10 How to change the adduct ion in use
4-11 Change the colour of unmeasured points (including transparency)
4-12 If you want to know the number of data points (area) within an ROI
4-13 If the IMDX file cannot be imported with error code 1101
4-14 FT-MS data conversion
4-15 MS/MS spectral normalization function
4-16 Batch copy or export of multiple images from MS Image List
4-17 How to retrieve PCA result
4-18 Partial Least Square (PLS)
4-19 Reducing the data size
4-20 How to create an MS image only within ROIs
4-21 MS image with overlaid ROI
4-22 Scale
4-23 TOF-MS data conversion
4-24 Setting ROI based on a specific m/z image
4-25 Convert Thermo fisher RAW file
4-26 How to convert imdx file to imzML file
4-27 When double-clicking the icon for IMAGEREVEAL MS, a “Missing Shortcut” is displayed.
5. Others
5-1 Making imzML from various type of files
5-2 Data conversion actual result
5-3 Centroid or Profile?
Sample data download
- Mouse liver sample data (for Basic Analysis) Mouse_Liver_Basic.zip
- Mouse liver sample data (for Quantitative Analysis) Mouse_Liver_Quant.zip
- Mouse testicle sample data (for Differential Analysis and Image Analysis) Mouse_Testicle.zip
- Yeast sample data (for Screening) Yeast_Screening.zip
Data format/data conversion
IMAGEREVEAL MS can read IMDX files.
The following 3 file formats can be converted to IMDX files using the “IMDX Converter” function included in this software.
- Data conversion procedure
1. kbd
This is the data format of images acquired by the iMScope series of instruments.
- The kbd files acquired by iMScope series of instruments cannot be converted unless LCMSolution (Ver. 3.81 or later) has been installed.
2. Analyze 7.5
This is the format of data exported from the AXIMA series.
- Analyze 7.5 format data that has not been exported from the AXIMA series is not supported.
- Analyze 7.5 files can be converted to IMDX files if they have a total spot count no more than 38,000 spots and an m/z range of 5 to 500,000.
3. imzML
This is the common format of data for the MS imaging.
- This data format can be loaded directly into IMAGEREVEAL MS. When "Processed" type imzML format files are converted into IMDX files, interpolation is performed for the sampling interval that has been set (or peak width, if the centroid is set in the original data), and the profile data of the same sampling position for all measurement points is saved. For this reason, it does not precisely match the sampling position of the original data.
- "imzML" format data that is not exported from MALDI-7090 may not be convertible to an IMDX file. The ability to use "imzML" format data of instruments other than the MALDI-7090 has been confirmed, but the ability to convert all "imzML" format data files is not guaranteed. If you are using imzML format data, first check the operation using the demo version. →Data conversion actual result (English)（PDF file）
- The "imzML" format data consists of either "Continuous" or "Processed" type profile data. Operations using the "Processed" type centroid data have been confirmed with this product. However, when the centroid data is converted into IMDX format, it is converted into profile data. →Centroid or Profile?（PDF file）
- imzML files that can be converted to IMDX files have spot counts in the X and Y directions that are respectively no greater than 65,535 spots, and an m/z range of 5 to 500,000.
This software was developed as a result of collaborative research with Kyushu University's Innovation Center for Medical Redox Navigation and Mitsubishi Tanabe Pharma Corporation.
IMAGEREVEAL, iMScope TRIO, AXIMA and MALDI Solutions are trademarks of Shimadzu Corporation.
Windows is a registered trademark or trademark of Microsoft Corporation in the United States and/or other countries.
Intel, Intel Core and Xeon are trademarks of Intel Corporation or its subsidiaries.
Caution: Certain pretreatment methods or creation of samples to obtain or process data with this software may require license permission from a third-party patent holder.
(Installation of this software does not constitute such permission.) As regards the necessity of licensing from third-party patent holders, we recommend consultation with an expert or the holder of the patent rights.