We use different protocol to clear our organ like X-clarity, CUBIC, RapiClear etc… But we have some problem with the DNA Staining. I measure that we stained with DAPI +/- 600 µm. The majority of our samples are bigger than 6 mm.
Do you have some probes that work better than DAPI ?
I’ve seen good results using TO-PRO3 in the context of iDISCO+
iDISCO+ protocol: https://idisco.info/
Original paper (figure 4): https://www.cell.com/cell/fulltext/S0092-8674(14)01297-5
Full penetration into a half brain is easily acheivable.
Assuming your clearing is good, the problem with DAPI is that at lower wavelengths there is usually more scattering and autofluorescence. TO-PRO3 is in the far red region of the spectrum where there is less scattering and autofluroescence. Hence, better contrast deep in cleared samples.