Figure 4

Frangi-based orientation analysis of myelinated fibers in a mesoscale tiled TPFM reconstruction (final stitched size: 8859.9 \(\upmu {\hbox {m}} \, \times\) 5204.8 \(\upmu {\hbox {m}} \, \times\) 98.0 \(\upmu {\hbox {m}}\), acquisition time: 14h 12min) of a brain region in between the primary and secondary visual cortex (V1/V2): (a) multichannel image (fibers: \(\lambda\) = 482 nm, cell bodies: \(\lambda\) = 618 nm) aligned and fused using ZetaStitcher (scale bar: 0.5 mm)^28,29, following the uneven illumination correction achieved via the CIDRE method³⁰; (b) myelinated fiber ODF map (\(\lambda\) = 482 nm) returned by the image processing pipeline (\(\alpha\) = 0.001, \(\beta\) = 1, scales = 1.25, 2.5 \(\upmu \hbox {m}\); ODF super-voxel: 80 \(\upmu {\hbox {m}} \, \times\) 80 \(\upmu {\hbox {m}} \, \times\) 80 \(\upmu \hbox {m}\)); (c) MIP of a 10 \(\upmu \hbox {m}\)-deep section including grey matter (green square, scale bar: 50 \(\upmu \hbox {m}\)); (d) corresponding grey matter ODFs (super-voxel: 10 \(\upmu {\hbox {m}} \, \times\) 10 \(\upmu {\hbox {m}} \, \times\) 10 \(\upmu \hbox {m}\)); (e) MIP of a 10 \(\upmu \hbox {m}\)-deep section including white matter (red square); (f) corresponding white matter ODFs (super-voxel: 10 \(\upmu {\hbox {m}} \, \times\) 10 \(\upmu {\hbox {m}} \, \times\) 10 \(\upmu {\hbox {m}}\)). Fiber ODF maps were displayed using the open-source software package for medical image processing and visualisation MRtrix3³¹.