How cells in the developing or adult brain are organized and behave following injury or disease remains a fascinating, yet still poorly understood, question. For many years, the ability to visualize the structural composition or global patterns across the neuro-axis of the adult vertebrate brain was limited by the lack of imaging tools available to examine cell phenotypes in larger tissue structures in situ in 3-dimensions (3-D). As a result, most interpretations have been derived from 2-dimensional (2-D) analyses of sectioned tissue. Recently however, the field of macro-imaging has become popularized by a growing interest of researchers to understand whole organ development, structure, and the associated morphological and cellular abnormalities that arise with disease (Short et al., 2010; Epp et al., 2015; Lloyd-Lewis et al., 2016; Short and Smyth, 2016). This has been paralleled by innovations in modern clearing techniques and specialized imaging methods designed to visualize thick tissues or whole organs in 3-D space, giving way to a new era of fluorescent, whole organ imaging (Susaki et al., 2014; Azaripour et al., 2016; Susaki and Ueda, 2016; Aswendt et al., 2017; Whitehead et al., 2017).

The value of macro-imaging has been demonstrated across a range of tissues, including embryos (Sharpe et al., 2002; Sharpe, 2003), heart (Kolesová et al., 2016; Aguilar-Sanchez et al., 2017), kidney (Short et al., 2010; Combes et al., 2014; Short and Smyth, 2016, 2017), lymph node (Song et al., 2015), mammary glands (Lloyd-Lewis et al., 2016), and brain (Gleave et al., 2013; Ode and Ueda, 2015), leading to new insight into the cellular behavior of organs under diverse conditions. This progress has been facilitated by the power of multiphoton imaging, newer confocal microscopes with lasers having increasingly better z-axis penetration, the development of light-sheet microscopes, and tomographic techniques such as Optical Projection Tomography (Sharpe et al., 2002; Keller et al., 2010; Parra et al., 2012; Kromm et al., 2016; McGowan and Bidwell, 2016; Susaki and Ueda, 2016; Whitehead et al., 2017). Nevertheless, whole organ imaging of thick tissue of ~1 mm or greater introduce a number of challenges that must be overcome compared to antibody labeling and confocal imaging of sectioned tissue at the micron scale.

In most cases the biggest obstacle for macro-imaging is the successful sample preparation of thick tissue or organs. A significant challenge continues to be the balance between homogeneous fluorescent labeling through the tissue block and rendering the tissue clear for imaging. Unfortunately, this can only be accomplished by trial and error, with individual tissue types having their own unique set of physical properties. Commonly protein labeling using antibodies or transgenic reporter lines, such as Green Fluorescent Protein (GFP), show excellent fluorescent signal prior to clearing steps. However, reagents used for transitioning tissue to a cleared state often reduce fluorescence levels or quench fluorescence altogether. To circumvent this problem, a variety of different tissue clearing methods have been developed, making use of CLARITY-based methods (i.e., PARS, PACT; Chung and Deisseroth, 2013; Yang et al., 2014; reviewed in Vigouroux et al., 2017), aqueous methods (i.e., CUBIC, Scale; Susaki et al., 2015), and non-aqueous methods such as 3DISCO (Belle et al., 2014, 2017; reviewed in Vigouroux et al., 2017), iDISCO (Renier et al., 2014), uDISCO (Pan et al., 2016), and BABB (Ahnfelt-Rønne et al., 2007). While the success of these methods appear to vary by tissue, some indeed show promise for preserving fluorescence for downstream imaging.

Many of the above clearing methods have been established specifically for studies of neural-circuitry or cell-specific analysis in the mammalian brain (Parra et al., 2012; Chung and Deisseroth, 2013; Susaki et al., 2014; Epp et al., 2015; reviewed in Azaripour et al., 2016; Vigouroux et al., 2017). However, the large size of the adult brain of rodent models, can limit imaging options or restrict imaging of the brain to only a specific subregion during a single scan. Unlike the rodent brain, the smaller brain of teleost fishes such as zebrafish and medaka, show exceptional promise as experimental models to visualize spatial changes along the 3-D neuro-axis in adulthood under physiological or compromised states. Having the opportunity to investigate cell dynamics within a 3-D context offers the chance to address novel questions concerning cell-specific behavior, systemic signaling, stem cell niche development, and morphological variation.

The zebrafish, in particular, has become a rising star in the field of adult neurogenesis, plasticity, and regeneration (Kaslin et al., 2008; Kizil et al., 2012; Lindsey and Tropepe, 2014; Lindsey et al., 2014; Than-Trong and Bally-Cuif, 2015; Alunni and Bally-Cuif, 2016; Ghosh and Hui, 2016). Constitutively cycling adult neural stem cells are found across an extensive number of neurogenic compartments along the anterior-posterior (A-P) neuro-axis (Adolf et al., 2006; Grandel et al., 2006; Chapouton et al., 2007), with these cells capable of producing newly regenerated neurons following brain injury (Kroehne et al., 2011; Baumgart et al., 2012; Kishimoto et al., 2012; Kyritsis et al., 2012; Kaslin et al., 2017). With its well mapped neurogenic niches, heterogeneous mixture of adult stem cell populations (Ganz et al., 2010; Lindsey et al., 2012), array of cell-specific transgenic lines, molecular toolbox, and highly conserved genome compared with its vertebrate counterparts, the zebrafish provides an exquisite experimental system to uncover clues governing stem cell dynamics under homeostasis and regeneration. However, there has yet to be developed a straightforward method to label and visualize adult stem cell populations in a 3-D context. While highly transparent zebrafish mutants lacking skin pigmentation, such as casper and crystal, have been made available in recent years, these lines only benefit imaging of larvae or early juvenile stages (White et al., 2008; Antinucci and Hindges, 2016), but do not mitigate opacity and light scattering in the adult brain. As a result, developing new clearing and imaging methods permitting 3-D visualization of changes in cell proliferation tailored for the adult zebrafish brain are needed. Therefore, the rationale for establishing the protocol described herein was to develop an efficient and feasible method to visualize and analyze actively cycling adult stem cells in their respective niches, in order to understand how they respond at a global scale to brain injury or when shifted from a homeostatic state.

Our protocol describes an 8-step method for sample preparation in advance of Optical Projection Tomography (OPT) imaging. The protocol takes advantage of the small molecular size of 5-ethynyl-2′-deoxyuridine (EdU) to reliably label cells in the S-phase of the cell cycle and uses individual reagents to avoid the high cost of the commercial “Click-it EdU kit” for staining (Salic and Mitchison, 2008). Clearing of the entire adult zebrafish brain without loss of EdU fluorescent signal is completed using a combination of benzyl benzoate and benzyl alcohol (BABB, also known as “Murray's reagent”), inexpensive, non-aqueous reagents that have been successfully demonstrated to render tissue transparent (Miller et al., 2005; Zucker, 2006; Short et al., 2010; Gleave et al., 2012, 2013). Unlike many lengthy labeling and clearing protocols for thick tissue, our pipeline allows for the proliferative pattern of samples to be readily visualized and analyzed in less than 10 days using software such as IMARIS or FIJI/IMAGEJ. Moreover, following EdU staining, we highlight that the option of whole brain fluorescent labeling of proteins or transgenic reporter lines can be performed, broadening the applications of this protocol. Finally, we present three analysis methods that can be applied to reconstructed OPT-scanned brain samples that can be completed using FIJI/IMAGEJ. OPT allows fluorescent or non-fluorescent imaging of paraformaldehyde fixed specimens with thicknesses of up to ~15 mm at near cellular resolution (3.21 um/pixel; Sharpe et al., 2002). Three or more fluorescent channels can be sequentially scanned from ultraviolet to infrared (i.e., 350, 488, 555, 647), in addition to brightfield, that can be reconstructed to obtain a 3-D or 2-D view of brains for manipulation. OPT has the added advantage over many newer microscopy techniques in obtaining isotropic datasets that are designed for 3-D volumetric analysis and morphometrics. Taken together, this protocol is the first of its kind to offer a streamlined method of whole brain imaging in the adult zebrafish brain, with the potential to be applied to other small teleost models (i.e., medaka and killifish) or for imaging using modern light-sheet microscopy.

All animal experiments were assessed and approved by the Monash University Animal Ethics Committee and were conducted under applicable Australian laws governing the care and use of animals for scientific research. Zebrafish (Danio rerio) were maintained in line with standard protocols at the Monash University FishCore.

Medaka (Oryzias latipes) stocks were maintained at the Institute of Toxicology and Genetics (ITG) of the Karlsruhe Institute of Technology (KIT). Animal husbandry and experimental procedures were performed in accordance with local and European Union animal welfare standards (Tierschutzgesetz 111, Abs. 1, Nr. 1, AZ35-9185.64/BH). The facility is under the supervision of the local representative of the animal welfare agency.

A summary of the workflow for parts 1–8 is shown in Figure 1A along with representative images of specific steps in the protocol. To facilitate laboratories in adopting this protocol, we have additionally designed a video demonstrating these key steps and procedures (Supplementary Video 1).

Three-dimensional fluorescent macro-imaging of whole organs is becoming commonplace in biology, providing new perspectives on how organs, tissues, and cells develop and respond to trauma or disease (Lupperger et al., 2017; Whitehead et al., 2017). Within the field of neuroscience, the existence of few practical methods to visualize the mature vertebrate brain in a 3-D context has hindered progress in understanding global patterns of change across cell populations following manipulation. The protocol illustrated here provides the neuroscience community with an innovative, simple method to visualize brain-wide patterns of cell proliferation along with brain morphology by taking advantage of the small size of the adult brain of the zebrafish model, the consistency of EdU labeling, and the isotropic nature of Optical Projection Tomography (OPT). Additionally, our OPT pipeline allows for the possibility of combining EdU staining with transgenic reporter lines and/or antibodies. Moreover, we demonstrate that reconstructed datasets can be easily quantified using freeware such as FIJI/IMAGEJ using EdU intensity or volume as output to examine broad patterns of change or within specific neuroanatomical domains of interest. The data can also be used as a building block to create a 3-D atlas and for standardization of expression patterns. Collectively, these features will establish this protocol as a valuable tool in small teleost models such as the zebrafish, to unveil new clues underlying brain-wide stem cell behavior during the regenerative process, new information underpinning systemic cell signaling of stem and immune cell populations, as well as tracking stem cell niche development and changes in brain morphology.

The successful labeling of proliferating stem/progenitor cells in the adult zebrafish brain in the current protocol depends largely on the properties of 5-ethynyl-2′-deoxyuridine (EdU). EdU has evolved as a modern alternative to the use of previous thymidine analogs, 5-bromo-2'-deoxyuridine (BrdU), 5-chloro-2'-deoxyuridine (CldU), and 5-iodo-2'-deoxyuridine (IdU), for labeling active DNA synthesis (S-phase) of the cell cycle (Salic and Mitchison, 2008). Moreover, unlike BrdU protocols, EdU labeling does not require DNA denaturation using harsh chemicals such as hydrochloric acid that often degrades tissue (Buck et al., 2008). Rather, EdU staining uses a rapid click-chemistry reaction between an azide (part of staining solution) and an alkyne (bound to EdU), allowing cryosectioned tissue to be labeled at room temperature in <30-min, and in the case of the whole adult zebrafish brain, within 4-days. The small size of the Alexa Fluor azide is readily accessible to the DNA, unlike larger anti-BrdU primary antibodies, making it well suited for penetration into thick tissue during the staining process. Importantly, EdU fluorescence is not degraded by methanol dehydration or BABB clearing like many other markers (Figures 2I–K), making it ideal for whole brain imaging and resulting in consistent labeling patterns in line with conventional cryosectioned tissue (Figures 2E,G).

Effective use of this protocol for sample preparation of zebrafish or other small vertebrates with comparable adult brain size requires attention and expertise at a number of different stages. Proper EdU administration is crucial for visualization of this marker during OPT imaging, and it is most cost effective to inject intraperitoneally as described. However, bath application in EdU can also be considered using the same chase periods presented here. In cases where this protocol is considered in juvenile animals, intraperitoneal microinjection of EdU or bath application must be performed due to the small size of fish. Proceeding EdU chase periods, brain dissection may be one of the more technically challenging steps. Nevertheless, time should be taken to remove the entire brain intact and ensure no debris (i.e., pigment, blood, tissue) remains on the surface before transfer into fixative (Figures 1C,D). Debris will impede the passage of light through the sample during OPT imaging, resulting in poor reconstructions and inaccurate analysis.

Without exception, embedding the EdU stained brains in the 6-well plates is the most important step of the protocol. Poor embedding will result in unusable samples even if the EdU labeling appears unspoiled. Thus, it is advisable that when starting this protocol for the first time, only 1–2 brain samples are embedding at a time in low melting agarose (Figure 1F). Agarose embedding has long been used in zebrafish research for histology of fixed specimens (ZFIN; Tsao-Wu et al., 1998; Copper et al., 2017) or live in vivo confocal imaging of larvae (Kaufmann et al., 2012), and is commonly used during sample preparation for OPT scanning across leading animals models, including but not limited to adult Drosophila (McGurk et al., 2007), mouse embryos and kidney (Sharpe et al., 2002; Short et al., 2010), and human brain tissue (Kerwin et al., 2004). Once the agarose begins to set there is a very narrow window of time to orient brains properly and smoothly without damage. Paramount is that brain samples do not fall to the bottom of the well, as this will place them outside the field of view when OPT imaging. Taking time to observe the samples in the z-plane of the well by looking at the side of the 6-well plate provides a good indication if brain samples are properly oriented. Lastly, before trimming the block always confirm which type of OPT mount will be utilized as this might require modifications to how the block is trimmed. Moreover, applying this protocol to other types of imaging, such as light-sheet microscopy, may necessitate slight deviations.

Those interested in taking advantage of the present protocol should make it common practice to run preliminary experiments and determine experimental parameters for downstream analysis prior to commencing OPT imaging. The importance of this cannot be overlooked, especially if the intensity of EdU is to be a measured output as we show with our Histogram Analysis (Figure 4). For instance, lesioned brains have considerably greater EdU intensity compared to control levels as a consequence of greater cell proliferation following injury (see Figures 4C, 6B–F). As a result, confirming a consistent level of exposure for both treatments that does not lose data in controls, nor over-expose data in the damaged brains must be done a priori. Similar to confocal imaging of immunohistochemical stained tissue, each sample will have slight variations in EdU intensity. Using a sample size of n = 5–10 animals in most cases allows for a reliable pattern to be extracted following post-processing.

Whole organ imaging produces large datasets (>1 GB) and often requires specialized quantification tools and powerful software to extract cell counts, staining patterns, or global trends from 3-D tissue. FIJI/IMAGEJ, IMARIS, and MATLAB are some of the more commonly available software programs that can be used to create 2-D or 3-D analysis methods to quantify reconstructed OPT datasets. In this paper we showcase three simple downstream analysis methods we developed exclusively in FIJI/IMAGEJ to examine the A-P profile of EdU intensity (Histogram Analysis: Figure 4) and EdU volume in large tissue regions of the adult brain (Structure Analysis: Figure 5) or tightly demarcated adult proliferation zones (Slice Analysis: Figure 6) following telencephalic lesion. While sophisticated computational methods to normalize 3-D expression data for standardized neuroanatomical maps are emerging in the larval zebrafish following live imaging (Randlett et al., 2015), not surprisingly, few analysis pipelines currently exist to analyze 3-D output derived from the adult zebrafish brain (Lupperger et al., 2017).

Although some modern OPT scanners are capable of single cell resolution, most provide datasets with only near cellular resolution. Undoubtedly this has limitations on how downstream analysis is performed on reconstructed OPT output. Given this, we view our EdU staining OPT pipeline as a starting point to visualize brain-wide trends in cell proliferation under varying conditions to identify neuroanatomical domains of interest that can subsequently be studied at the single cell level using immunohistochemistry, in situ hybridization, or electron microscopy on sectioned tissue. Analysis of mouse kidney has previously shown that OPT tissue is compatible with physical sectioning for immunostaining and transmission EM, allowing users to seamlessly move from one technique to the next within a single sample (Combes et al., 2014). Here we illustrate that both EdU intensity and EdU volume are informative and reliable methods to represent and quantify OPT data to investigate systemic changes in the CNS post-injury. In particular, we highlight that EdU volume derived from OPT scans is a statistically detectable readout to compare changes in EdU staining between the uninjured and injured brain.

Our combined Histogram and Structure analyses bring to light that the systemic response of cell proliferation to forebrain injury is apparent along the entire length of the neuro-axis and peaks at 1-dpl across all structures distal to the lesioned hemisphere (Figures 4C, 6B–I). However, these analyses encompass all cells that have entered a proliferative state, which is known to include a significant population of immune cells that are activated upon injury and present in the tissue parenchyma (Kroehne et al., 2011; Kyritsis et al., 2012; Kaslin et al., 2017). Comparing these findings with the results from our Slice Analysis, we observed that lesion-induced signals do not appear to modulate the degree of cell proliferation in the proliferative domains of posteriorly located tectal and cerebellar structures (Figures 6N–Y), but rather remains proximal to the lesioned and unlesioned hemisphere (Figures 6B–M). The dichotomy in the pattern of change in EdU observed between Histogram/Structure Analysis and Slice Analysis imply that cues from the lesion site differentially activate populations of adult neural stem cells in stem cell niches positioned along the A-P axis, but trigger global proliferation of leukocytes in the brain parenchyma.

Beyond studies of global changes in EdU following traumatic brain injury, we show that our OPT protocol has merit for uncovering new clues related to stem cell niche development and brain morphology. By combining larval whole brain confocal imaging of EdU (Figures 7A–C) with EdU labeling using our OPT pipeline (Figures 7D–F) we are now able to visualize the localization of cell proliferation over the full spectrum of zebrafish development into senescence to track the proliferative status of individual life-long proliferation/growth zones. We see this work as a fundamental starting point to transition towards being able to obtain isotropic 3-D data of specific gene expression patterns in the adult CNS that can be used to create standardized brain maps and bridge the gap between embryonic, larval, juvenile and adult shape and morphology. Likewise, coupling whole brain imaging of developing adult stem cell niches with cell-specific markers, methods such as immuno-correlative light and electron microscopy, and niche-specific transcriptomics will be a powerful approach to dissect how distinct niches are constructed and regulated at key developmental milestones. Secondly, we show that our OPT pipeline can readily be adapted to other small experimental fish models, such as the medaka, for comparative studies of brain morphology and cell proliferation (data not shown). Taking advantage of brain autofluorescence that can be imaged during OPT scans, we reveal that this is a tractable method to obtain morphometric scans of brain volume for quantitative analysis. By directly testing the feasibility of this approach in three inbred strains of medaka (Figures 8A–F), we demonstrate that differences in the volume of distinct brain structures can be quantified using IMARIS volumetric algorithms (Figures 8G,H). We envision this approach to be highly desirable to the medaka community to progress current knowledge on the genetic basis of brain development as a result of the high tolerance of this species to inbreeding (Kirchmaier et al., 2015).

Optical Projection Tomography was first designed to study gene expression patterns in the developing mouse embryo (Sharpe, 2003). Over the last 15-years OPT has played a pivotal role in answering a diversity of biological questions primarily in rodent models (Vinegoni et al., 2009; Short et al., 2010; Jeansson et al., 2011; Gleave et al., 2012, 2013; Anderson et al., 2013; Combes et al., 2014; Short and Smyth, 2016, 2017), using commercially available or custom built OPT systems (Wong et al., 2013). Here, we have optimized an EdU sample preparation pipeline for the adult zebrafish brain taking advantage of the tomographic imaging of OPT with the aim of expanding our knowledge of adult stem cell behavior following traumatic brain injury. We show that output from OPT scans can be examined quantitatively using FIJI/IMAGEJ to identify systemic changes in cell proliferation post-injury, and that our OPT pipeline would serve as a beneficial imaging tool to track stem cell niche development over ontogeny and study changes in brain morphology. Moving forward we welcome collaborations from members of the teleost community (zebrafish, medaka, or other) and hope this protocol will be of practical use for many laboratories.

The protocol presented here was developed by BL and JK for zebrafish, in collaboration with FL for its application with medaka. BL was responsible for drafting the manuscript and figures with conceptual input from both JK and FL. AD was responsible for EdU staining and larval whole brain confocal imaging in zebrafish. AD and BL performed all revisions to figures and the inclusion of additional data in the manuscript. BL and JK were responsible for the creation of supplementary videos accompanying the manuscript.