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Tissue Clearing:


Imaris analysis:


Validated antibodies:

Antigen Host Vendor Catalog Dilution Type of staining
Calbindin Rabbit Swant CB -38a 1:15000 3DISCO
Cfos Rabbit Synaptic Systems 226003 1:500 iDISCO
CHX10 (VSX2)
Sheep Abcam ab16141 1:500 3DISCO
CTIP2 Rat Abcam ab18465 1:100 iDISCO
GFP Rabbit Invitrogen A11122 1:1000 3DISCO 
Islet1 Goat Neuromics GT15051 1:2000  3DISCO
L1 Rat Milipore MAB5272 1:500 3DISCO
Netrin Rabbit Abcam ab126729 1:500 3DISCO 
Nrp2 Goat R&D AF567 1:1000 3DISCO
Pax6 mouse DSHB pax6 1:200 iDISCO
pHH3 Rabbit Cell Signaling 9701  1:800 3DISCO 
RFP Rabbit Rockland 600-401-379 1:1000 iDISCO
Robo1 Goat R&D AF1749 1:300 3DISCO
Robo3 Goat R&D AF3155 1:300 3DISCO
Satb2 Rabbit Abcam ab34735 1:200 iDISCO
Six3 Rabbit Rockland 600-401-A26 1:500 3DISCO
TH Sheep Pelfreez P60101-150 1:500 3DISCO 
TH Rabbit Millipore AB152 1:1000 3DISCO  / iDISCO
TrkA Goat R&D AF1056 1:400   3DISCO
TrkC Goat R&D AF1404 1:400  3DISCO 


Considerations for the choice of secondary antibodies:

Laser wavelength

Suggested fluorophore



488 nm

Alexa Fluor 488, Cy2

Compatible with the 561 and 647 nm laser.

Highest autofluorescence.

Least preferred channel for imaging.

561 nm

Alexa Fluor 555, Alexa Fluor 568, Cy3, Cy3.5

Strong laser power; Compatible with 488 and 647 nm lasers.

Reasonable amount of autofluorescence.

647 nm

Alexa Fluor 647, Cy5

Very low autofluorescence; strong light penetration; strong laser power; Compatible with 561 and 488 nm lasers.

Most recommended channel for imaging.

730 nm

Alexa Fluor 750, Cy7

Almost no autofluorescence; strong light penetration.

Weak laser power

Note: The 730 nm laser is positioned in a separate beam combiner which might cause minor alignment variations in the light sheet angles. Pixel-based co-localization analysis should not be performed with this laser.