Instructions

Please read the user manual in its entirety if you are new to MSiReader v3.12. It will improve your understanding of the software and how to best use it to effectively support your research. Every “§” is a hyperlink to a section within the user manual to assist in navigation. Every italics word is a variable in the preferences INI file (§5) for which the default can be changed to customize the user’s experience. There are ToolTips embedded within the program that are displayed by a mouse over and a brief hover on a GUI object – a description about the tool or data to be entered is provided. The user manual is provided as a PDF file (See “user guide” under the Help pull-down menu in MSiReader) as well as an online PDF and HTML version at

https://msireader.com/docs/MSiReader_UserManual/

Video Tutorials are posted at https://msireader.com/tutorials and Test Datasets are posted at https://msireader.com/support

New videos and test data sets are being added regularly so please check the website frequently. MSiReader test datasets are provided so that users can follow the user manual and/or the video tutorials. However, it is highly recommended that you move the test data sets to your local hard drive prior to testing out the software.

IMPORTANT: There are many parts of MSiReader that will allow the user to export/save a new .imzML, a *.mss or a *.mim file (these are MSiReader’s custom formats). If the user loads an imzML dataset, they can save it a new imzML file; however, if a user loads a native file (e.g., *.raw file from a Thermo instrument), the user can then save this as a *.mss or a *.mim file. Importantly, once a user does this within MSiReader, these files are no longer usable in third party software. For newly created imzML files within MSiReader, the end-user MUST keep the .ibh file in the same folder as the new .imzML to be read.