NanoT - The TUM NanoSIMS Toolbox

User friendly tool to automatically pre-process NanoSIMS Indexed Mesh (IM) files. This software was created as part of the TUM SoilCarbonHack project. Note that this is still work in progress and only a beta version. Improvements and additional features are on the way. For feedback and issues, please mail to: maximilian.zollner@tum.de

Download

You can download the current version’s (NanoT-beta-1.1.0) installer for Windows OS here: DOWNLOAD

Minimal Usage

Run the installer and execute NanoT from the start menu. Then, give input and output directory for your IM files, and chose at least one output file format. Finally, press the start button to run the processing.

Why use this?

• enables automated batch processing of raw data
• variety of possible output file formats: HDF5, TIF, NPY, NRRD, JPG
• search directories recursively
• straightforward usage, easy to install, and no additional software packages necessary
• metadata can be read directly from IM files and saved within HDF5 or log files
• possibility to exclude pre-processing steps

Default Processing Scheme

The tool will run the following steps in the given order:

1. Dead-time correction
2. Raster correction
3. Alignment
4. Sum image creation

Changelog

NanoT-beta-1.1.0

• name change from appSIMS to NanoT
• new splashscreen
• new launcher (and removed vbs and bat scripts)
• minor bug fixes

NanoT-beta-1.0.1

• bug fix for progress bar
• bug fix for multiple runs during single session

NanoT-beta-1.0.0

• NanoT can run multiple times within a single session
• splashscreen update
• window resizing and maximizing disabled
• recursive search for files
• interpolation disabled for JPEGs
• layout improved

NanoT-alpha-1.1.0

• fix for bug where NRRD files could not be read by external software
• file and directory browser
• new GUI layout
• progress bar
• VBS script to start and all scripts converted to PYW to surpress console
• output is now redirected to conosole in GUI
• NanoT.pyw (NanoT.py+gui.py)
• splash screen

NanoT-alpha-1.0.3

• NSIS script: name, start menu shortcuts, tum-bgd instal directory

NanoT-alpha-1.0.2

• license and license bundle
• catched FileNotFoundError
• README.html
• removed several site-packages
• fix for error “ChampsList is non-null, dont know how to read.”

NanoT-alpha-1.0.1

• output formats nrrd and jpg
• options to disable preprocessing steps
• possibilty to create multiple outputs at once
• fix for roll bug
• fix for calibration date bug
• full GUI
• NSIS installer and uninstaller
• option for h5 dataset name
• VERBOSE option for all text outputs
• options to exclude metadata

NanoT-alpha-1.0.0

• initial version for a tool to automatically preprocess nanosims data
• console dialog for input path, output path, and output format
• options for output format: TIF, HDF5, NPY