Softworx imaging program

The high-resolution fluorescence microscope Delta Vision Elite Imaging System (GE healthcare) was used to analyze all immunofluorescence staining experiments. Images were acquired using a scientific complementary metal-oxide-semiconductor (sCMOS) camera and obtained using three different filters at different wavelengths: 488 nm (green), 594 nm (red) and 647 nm (purple, which we digitally changed into blue to have a better contrast with the green and red signals). Images were finally processed with Softworx imaging program (Applied Precision). For imaging adhered bacteria, human cells (SH-SY5Y, differentiated neurons and primary neurons) were fixed and not permeabilized, only the plasma membrane was imaged with a single snapshot for each filter. For imaging intracellular bacteria in differentiated neurons, or bacterial interaction with neurons in mouse brain sections, series of z-stacks were imaged in order to capture either the thickness of the neurons (in case of imaging differentiated neurons) or the cell morphology of neurons within each brain mouse section. The z-stacks Images (z-stacks) taken with the DV Elite Imaging System was rotated using the 3D Volume Viewer function of the imaging software Softworx.

Microscopic analysis was performed using a DV Elite microscope (Applied Precision Ltd.). The z-stack images were acquired using a scientific complementary metal-oxide semiconductor (sCMOS) camera and processed with SoftWoRx imaging program (Applied Precision Ltd.). Images (z-stacks) taken with the DV Elite Imaging System have been rotated using the 3D Volume Viewer function of the imaging software SoftWoRx.