Table 2.
Summary of optical clearing techniques used in neurodevelopment studies.
| Specimen | Species | Age | Technique | Cell Type/ Structure/ Marker | Citation | ||
|---|---|---|---|---|---|---|---|
| Development | Neurogenesis | Whole Brain | Zebrafish | 3. 5. 7DPF/6-12M | BABB | Proliferating stem cells, glia, GFP-reporter | Lindsey et al, 2018 |
| Whole Brain | Xenopus/Tg Xenopus | Stages NF45 (1 week old) & NF46/47 | CLARITY | Oligodendrocytes, neurons, nuclei, mitotic cells | Fini et al, 2017 | ||
| Proliferation | Brain | Xenopus/Zebrafish/Chicken | E15/P0/4W/Adult (1-3Y)/ Adult (3M-2Y) | CLARITY PACT | TH Immunoreactive cells, nuclei, 5-HT+ CSF-c cells, DA+ cells, TH1+ cells, TH2+ cells | Xavier et al, 2017 | |
| Connectivity/Circuitry/Tracing/Mapping | Whole brain Brain | Mouse/Tg Mouse | 2-3M | CLARITY | Membrane-localized proteins, dendritic spines, synaptic puncta, neurons, axonal fibers | Chung et al, 2013 | |
| Brain Spinal cord | Mouse | 12–14W | CLARITY | Raphe nuclei, reticular nuclei, BDA fibers, raphespinal fibers, serotonergic fibers | Liang et al, 2015 | ||
| Whole brain Whole spinal cord | Tg Zebrafish/Tg Mouse | Larva | CLARITY | Neurons | Tomer et al, 2015 | ||
| Brain | Mouse | P70 | tB-BABB | Subcortical nuclei, neurons, dendrites, glia, axons | Schwarz et al, 2015 | ||
| Brain | Mouse/Tg Mouse | Adult/P1-3/ ~8-12W | iDISCO+ClearMap | Axon projections, neurons, c-Fos+ cells- immediate early genes | Renier et al, 2016 | ||
| Brain Spinal cord | Tg Mouse/Rat | Adult | CLARITY | Nuclear DNA, astrocytes, and DiI labeled cells | Jensen and Berg et al, 2016 | ||
| Spinal cord | Mouse | - | CLARITY CUBIC | Serotonergic fibers | Liang et al, 2016 | ||
| Whole brain | River lamprey | Adult | CLARITY | Neurons, intemeurons, neurobiotin-injection, afferent and efferent projections | Kardamakis et al, 2016 | ||
| Brain | Tg Mouse | E0/E15.5/P0/P4 | iDISCO+3DISCO | Axons, ß-galactosidase in nuclei, trigemino-thalamic (TT) tract trajectory, c-Fos+ cells | Renier et al, 2017 | ||
| Brain | Mouse | 6-8W | SWITCH | Neurofilaments, blood vessels | Ren et al, 2017 | ||
| Brain | Tg Mouse | P42–49/ P70-80 | ScaleS | Astrocytes | Chai et al, 2017 | ||
| Brain | Mouse/Rat/Marmoset | 6W/3Y | CUBIC | Cell bodies, dendrites, neurons, microvasculature | Watson et al, 2017 | ||
| Brain | Tg Mouse | Adult | CLARITY2 | Purkinje neurons, dendrites, cell soma, neurites | Magliaro et al, 2017 | ||
| Whole brain | Mouse/Tg Mouse | 8-13W | CLARITY Whole Brain Openbrainmap | d3/d5 dendrites, cell bodies, neurons, intemeurons | Furth et al, 2018 | ||
| Whole mouse paw | Tg Mouse | E14.5/P0.5 | CLARITY | Fgfr1 expression/GFP/cell nuclei | Collette et al. 2017 | ||
| Whole Brain | Mouse/Tg Mouse | 3-6M | CLARITY | Myelinated WM tracts | Chang et al, 2017 | ||
| Brain Pancreas Whole Mouse | Mouse/TgMouse/Human | 91–117DPC/E15/P2-42/2–8Y | CLARITY | Neural projections, neurons, vasculature, pancreatic islets cells | Hsueh et al, 2017 | ||
| Brain | Mouse | E15/P21/P70 | SeeDB2G BABB 3DISCO | cortical neurons, mitral and tufted cells, axons, dendrites | Sakaguchi et al, 2018 | ||
| Whole fruit fly | Tg Fruit Fly | Pupae/Adult 4–5 days | FlyClear | Dorsal cluster neurons, medulla columnar neurons | Pende et al, 2018 | ||
| Brain | Mouse/Tg Mouse | 8-12W | uDISCO | Parvalbumin and somatostatin intemeurons, dopaminergic neurons, TH+ neurons | Lin et al, 2018 | ||
| Whole Brain Brain | Tg Mouse | 1W/3W/8W/10W/11W/4M/6M | CUBIC X ScaleCUBIC CUBIC-Atlas | Cell nuclei and spines | Murakami et al, 2018 | ||
| Brain | Tg Mouse | P5-80 | SeeDB2 | Microglia, purkinje cells, climbing fibers, liposomes, synapses | Nakayama et al, 2018 | ||
| Whole Mouse Whole Brain | Tg Mouse | Adult | uDISCO BABB 3DISCO vDISCO | Neurons, neurites, meningeal lymphatic vessels, microglia, axonal projections | Cai et al, 2018 * | ||
| Brain | Tg Mouse | P21 | SeeDB2 | Mossy fibers terminals, thorny excrescences, dendritic spines, pyramidal cells | Weng et al, 2018 | ||
| Whole Brain Brain | Rat/Sheep | Adult | iDISCO | TH neurons, nuclei, fibers, cell bodies, kisspeptin and NKB cells, KNDy cells, GnRH fbers | Moore et al, 2018 | ||
| Whole Brain | Zebra finches | Adult | CUBIC iDISCO+ | Vasculature, fiber tracts, nuclei | Rocha et al, 2019 | ||
| Brain | Mouse/Tg Mouse | 9W | FOCM | Neurons, neuron bundles, dendrites, synaptic boutons | Zhu et al, 2019 | ||
| Vascular Network | Brain Whole Spinal cord | Tg Mouse/Rat | Adult | PACT PARS | Endothelial cells, cell nuclei, glia, blood vessel, neurons | Yang et al, 2014 | |
| Retinal flat mount | Rats | P7/P14 | CLARITY | Vasculature, vertical sprouts, endothelial cells | Singh et al, 2017 * | ||
| Whole Brain | Mouse | 3M | 3DISCO | Vessels, capillaries, vascular wall | Todorov et al, 2019 | ||
| Migration | Brain | Piglet | 1W | iDISCO | Neuroblasts, migrating neuroblasts | Morton et al, 2017 | |
| Brain | Mouse | P11/15/16/29–31/55–57/Adult (3M) | TDE | Neuroblasts , mature neuronal cell nuclei, blood vessels, astrocytes | Aoyagi et al, 2018 | ||
| Brain | Ferret | P20/40/65/90 | iDISCO+ | Neuroblasts, migrating neuroblasts, SCGN+ cells, cell nuclei, myelin | Ellis et al, 2019 |
DPF, days post fertilization; M, months of age; Tg, transgenic or reporter; NF, nieuwkoop and Faber stage; E, embyronic day; P, postnatal day; W, weeks of age; Y, years of age; DPC, days post conception.
*
denotes publications that also use an injury model.