Open LabBot and RmsiGUI: Community Development Kit for Sampling Automation and Ambient Imaging

Abstract

Mass spectrometry research laboratories reported multiple probes for ambient ionization in the last years. Combining them with a mechanical moving stage enables automated sampling and imaging applications. We developed a robotic platform, which is based on RepRap 3D-printer components, and therefore easy to reproduce and to adopt for custom prototypes. The minimal step width of the Open LabBot is 12.5 µm, and the sampling dimensions (x, y, z) are 18 × 15 × 20 cm. Adjustable rails in an aluminium frame construction facilitate the mounting of additional parts such as sensors, probes, or optical components. The Open LabBot uses industry-standard G-code for its control. The simple syntax facilitates the programming of the movement. We developed two programs: 1) LABI-Imaging, for direct control via a USB connection and the synchronization with MS data acquisition. 2) RmsiGUI, which integrates all steps of mass spectrometry imaging: The creation of G-code for robot control, the assembly of imzML files from raw data and the analysis of imzML files. We proved the functionality of the system by the automated sampling and classification of essential oils with a PlasmaChip probe. Further, we performed an ambient ionization mass spectrometry imaging (AIMSI) experiment of a lime slice with laser desorption low-temperature plasma (LD-LTP) ionization, demonstrating the integration of the complete workflow in RmsiGUI. The design of the Open LabBot and the software are released under open licenses to promote their use and adoption in the instrument developers' community.

Contrast optimization of mass spectrometry imaging (MSI) data visualization by threshold intensity quantization (TrIQ)

“…The Otsu segmentation method ( Otsu, 1979 ) tested in this work comes with the R package EBImage ( Pau et al, 2010 ). Recently, we published an R-based platform for MSI data processing with a graphical user interface, RmsiGUI, which provides modules for the control of an open hardware imaging robot ( Open LabBot ), the processing of raw data, and the analysis of MSI data ( Rosas-Román et al, 2020 ). We integrated the TrIQ algorithm into RmsiGUI and provide the R code snippets for facilitating its adoption into other programs.…”

Mass spectrometry imaging advances and application in pharmaceutical research

“…Data collection mode: An industrialized robot system for automatic management of batch tissue samples, streamlined MSI data acquisition, and quality control is expected to establish a more standardized procedure. It is surprising to notice that effort has been made in this industrial design direction [115].…”

MeteoMex: Open infrastructure for networked environmental monitoring and agriculture 4.0

“…Initiatives such as the Public Lab (https://publiclab.org) and Lab On The Cheap (https: //www.labonthecheap.com) (Gibney, 2016), in contrast, promote the community-driven development of open technology. Such low-cost and do-it-yourself (DIY) devices are not only suitable for crowd-sourcing data in so-called citizen science (Dickinson et al, 2012), but also stateof-the-art research in the instrumental analysis (Martínez-Jarquín et al, 2016;Rosas-Román et al, 2020). Environmental sensing projects often use simple microcontroller boards such as Arduino (https://www.arduino.cc) and Wemos (https://www.wemos.cc) variants.…”