Computational protocol: Automated microbeam observation environment for biological analysis—Custom portable environmental control applied to a vertical microbeam system

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[…] A computer running the AMOEBA desktop client connects to the server module by a USB cable. The AMOEBA software records the data gathered by the sensors and sets up the bus to control the environment. Once gathered, the data can be saved either into a specific AMOEBA XML file or to a character separated file that can be read using a customised script or any commercial spreadsheet software. For more complex experiments, the AMOEBA desktop client is also capable of running customised Python scripts specific to the experiment. shows a screen shot from the AMOEBA software client which was written in Python 2.7 with the graphical user interface created using the PySide library (PySide, Qt, Santa Clara, CA) and Matplotlib [] used to create the graphs. [...] An AMOEBA environmental shroud () is used to create a controlled but not sealed volume above the cell dish and to hold sensors in place during experiments. The shroud was designed using FreeCAD (FreeCAD: An open-source parametric 3D CAD modeller) and constructed using 3D printing. The design can be modified and reprinted within 6 h at a cost of less than $10 by users who possess their own extrusion 3D printer using either extruded ABS or PLA, or a professional service could produce the design for a cost of approximately $100. In the AMOEBA system described in this paper, the shroud was printed using the Shapeways 3D printing service using their Strong and Flexible plastic (Shapeways, NY) using a powder bed method. Although the shroud is not biocompatible this is not an issue because it is never in contact with the cells. The chamber is also not sealed but the air flow out is greater than the airflow into the chamber and also the amount of CO2 required to maintain 5% atmosphere is very low (0.05 l per hour); but if desired it would be possible to design and build a sealed chamber if desired.This work uses a shroud designed around the RARAF microbeam endstation to validate the AMOEBA [,]. The RARAF environmental shroud allows for dual objectives as well as a removable side for easy removal and insertion of cell dishes. The external dimensions of the shroud are 12.3 cm × 12.3 cm × 2.3 cm, and it controls a volume of 167.4 cm3. To construct it uses a total volume of 157 cm3 of material to print with 100% infill. It is compatible with cell dishes with a diameter below 86 mm and could be easily be redesigned to cater for other plating systems if necessary without having to change any of the electronics. […]

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