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Cell and network volumes were created using the Imaris (Bitplane, Zurich, Switzerland) software package.
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Confocal images were processed using the Imaris program (Bitplane AG, Zürich, Switzerland) and Photoshop 6.0 (Adobe System Inc).
The PCNA-positive beta-cells were counted manually, while the counting of the EGFP-positive and RFP-positive cells were performed using the Imaris Imaging Software (Bitplane).
Colocalization analyses were performed using the Imaris colocalization module (Bitplane AG, Zurich, Switzerland).
Image data obtained were processed by using the IMARIS software package (Bitplane AG, Zürich, Switzerland).
Processes (filaments) and synaptic puncta within each section were traced in 3D using the Imaris 6.2 software (Bitplane).
Hippocampal mossy fiber boutons were reconstructed from image stacks using the Imaris surface tool (Bitplane, Zurich, Switzerland).
Confocal images of 18 biofilms were captured (ZEISS LSM780 Confocal System) and analyzed using the Imaris software package (Bitplane).
A × 40/1.3 NA (numerical aperture) oil-immersion objective lens was used with a zoom factor of 4. Images were analysed using the Imaris analysing software (Bitplane).
The average biovolume of biofilm formed per 7,228.4 μm of three technical replicates was calculated using the Imaris software package (Bitplane, AG).
Dendrites were traced semi-automatically using the Imaris Filament Tracer module (Bitplane) and thresholded colocalization of the ECM and dendrite signals was performed.
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