Comparison of fluorescence quenching between different neural labeling methods after 3DISCO (with BABB) tissue clearing
| Axonal/neuronal labeling with: | Fluorescence quenching | Ideal imaging time frame | Comments |
|---|---|---|---|
| AAV-eGFP, tdTomato | Fluorescence disappears progressively within a week | Within 48 h | eGFP is preferred over tdTomato |
| Fluoro-Ruby, Fluoro-Emerald | Fluorescence remains for few months | Within first few weeks | Results in off-target labeling of perivascular macrophages |
| CTB-conjugated to Alexa fluors | Fluorescence remains for few months | Within first few weeks | Preferentially labels cell body rather than axon; axon visualization requires software filtering |
| Whole-mount immunofluorescence with Alexa fluors | Fluorescence remains for few months | Within first few weeks | e.g., Whole-mount staining of embryos followed by tissue clearing |
Based on results from this study and our unpublished observations.