ArticleScientific reports2016
CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Fluorescent Labeling Methods for Brain Structure Research.Molecules (Basel, Switzerland) · 2026Review
- LFP-LOC: an LFP power-based method for validating the anatomical placement of high-density neural probes in rodents.Frontiers in neuroscience · 2026Article
- The Neurogenic Niche: Interactions Among Vessels, Glia, and Neural Stem Cells.Stem cells international · 2026Review
- A pipeline for mouse brain registration to an atlas after in vivo neurophysiological recordings.Anatomical science international · 2025Article
- FLUID: a fluorescence-friendly lipid-compatible ultrafast clearing method.Biomedical optics express · 2024Article
- Datasets assessing lipid-content in optically cleared brains.Data in brief · 2024Article
- A versatile vessel casting method for fine mapping of vascular networks using a hydrogel-based lipophilic dye solution.Cell reports methods · 2023Article
- Microvillar Cartography: A Super-Resolution Single-Molecule Imaging Method to Map the Positions of Membrane Proteins with Respect to Cellular Surface Topography.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Studying the trafficking of labeled trodusquemine and its application as nerve marker for light-sheet and expansion microscopy.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Article
- Multiregion neuronal activity: the forest and the trees.Nature reviews. Neuroscience · 2022Review
- Scalable tissue labeling and clearing of intact human organs.Nature protocols · 2022Review
- CCR7 signalosomes are preassembled on tips of lymphocyte microvilli in proximity to LFA-1.Biophysical journal · 2021Article
- Fluorescently Labeled PLGA Nanoparticles for Visualization In Vitro and In Vivo: The Importance of Dye Properties.Pharmaceutics · 2021Article
- Review
- Advancing Drug Discovery for Neurological Disorders Using iPSC-Derived Neural Organoids.International journal of molecular sciences · 2021Review
- Urea-based amino sugar agent clears murine liver and preserves protein fluorescence and lipophilic dyes.BioTechniques · 2021Article
- Rapid immunostaining method for three-dimensional volume imaging of biological tissues by magnetic force-induced focusing of the electric field.Brain structure & function · 2021Article
- Long-term labeling of microelectrode tracks with fluorescent latex microspheres.Journal of neuroscience methods · 2020Article
- hFRUIT: An optimized agent for optical clearing of DiI-stained adult human brain tissue.Scientific reports · 2020Article
- A gum Arabic assisted sustainable drug delivery system for adultBiology open · 2020Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorescent lipophilic dyes, such as DiI, stain cellular membranes and are used extensively for retrograde/anterograde labeling of neurons as well as for marking the position of extracellular electrodes after electrophysiology. Convenient histological clearing techniques, such as CLARITY, enable immunostaining and imaging of large volumes for 3D-reconstruction. However, such clearing works by removing lipids and, as an unintended consequence, also removes lipophilic dyes. To remedy this wash-out, the molecular structure of the dye can be altered to adhere to both membranes and proteins so the dye remains in the tissue after lipid-clearing. Nevertheless, the capacity of such modified dyes to remain in tissue has not yet been tested. Here, we test dyes with molecular modifications that make them aldehyde-fixable to proteins. We use three Dil-analogue dyes, CM-DiI, SP-DiI and FM 1-43FX that are modified to be CLARITY-compatible candidates. We use the challenging adult, myelin-rich spinal cord tissue, which requires prolonged lipid-clearing, of rats and mice. All three dyes remained in the tissue after lipid-clearing, but CM-DiI had the sharpest and FM 1-43FX the strongest fluorescent signal.
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