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Images were processed using the Leica application suite (version 2.8.1).
Image acquisition and analysis was done using the Leica Application Suite Software.
The labeled cells were subsequently viewed with a fluorescent (Leica DMI400B) microscope (Leica Microsystems, Heerbrugg, Switzerland) at 350 555 nm; images were captured using the Leica application suite Software.
For the CRT3-CFP images, one µm Z-stack sections were recorded (36 sections in total), which were merged to a single Z-stack image using the Leica Application Suite Advanced Fluorescence imaging software.
Time-lapse sequences of a single confocal optical section through the notochord were collected with an HCX plan APO 20x (NA 0.7) objective at 1 min intervals using the Leica application suite Advanced Fluorescence software.
This analysis was performed using confocal images from coronal sections at similar rostro-caudal levels (from bregma −1.70 mm to −3.00 mm) obtained with a Leica TCS SP5 laser confocal microscopy by using the Leica Application Suite (Advanced Fluorescente Lite 1.8.1).
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Acini area (mm) was measured using the Leica Applications Suite v.3.8.0 software.
After two PBS washes, samples were imaged at 10× on a Leica DM IL inverted microscope using the Leica Applications Suite software.
Chromosomes were counted in a drop of immersion oil at 100× using a Leica DM 2500 microscope equipped with a DFC 290 HD camera, using the Leica ver. 3 application suite software.
Mice infected with GFP-labelled bacteria were analysed using the Leica macrofluo instrument (Wetzlar, Germany) equipped with the Leica application suite 3.1.0 software.
Confocal stacks were taken using the Leica SP5 confocal microscope, 20x water immersion objective and Leica Application Suite (LAS) software.
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