TABLE 1.
Select methods used for anatomical phenotyping.
| Method | Live plant possible | Destructive | In situ/Ex situ | Advantages | Disadvantages | |
| Hand section | Brightfield microscopy (BF) | For a short period | Yes | Ex situ | High degree of sample manipulation; High Throughput | Unknown section thickness; varied quality |
| Confocal laser scanning microscopy (CLSM) | ||||||
| Agarose embedding for vibratome Sectioning | BF | For a short period | Yes | Ex situ | Wide range of specific section thickness possible; Fast; High Throughput | High attrition rate of embedded samples (for duckweed); Imaging must be done quickly to avoid deterioration |
| CLSM | ||||||
| Wax/Paraffin embedding for microtome sectioning | BF | No | Yes | Ex situ | very narrow sections; Fixed samples do not deteriorate | Lengthy fixing process; Loss of live cellular information; Some tissue types cannot be cleared; Lower Throughput |
| Clearing (ClearSee) | CLSM | No | No | In situ | Capable of capturing every cell in an individual in an image stack | Lengthy fixing process; fragile sections; loss of live cellular information; Lower throughput |
| Scanning electron microscopy (SEM) | No | No | In situ | Extremely high resolution 1–20 nm, clear image depth | Lengthy fixing process, loss of live information, samples must be able to handle vacuum pressure. | |
| X-ray computed microtomography (μCT) | Yes | No | In situ | Able to discriminate between materials; whole plant; 3D; Multiple 2D projections from a single scan | Lower throughput; Lower resolving power than electron/high resolution light microscopy | |
|
Method |
Minimum slice |
ACCESSABILITY |
Reference | |||
| thickness | ||||||
| Availability | Cost | Time | ||||
| Hand section | BF | 150 μm (Non-standard) | High | Low | Low | St. Croix et al. (2005), Thorn (2016), Huszka and Gijs (2019), Jonkman et al. (2020) |
| CLSM | 0.05 μm optical slices; 20–120 μm penetration | Medium | Medium | |||
| Agarose embedding” | BF | 75 μm | High | Low | Low | Atkinson and Wells (2017) |
| CLSM | 0.05 μm optical slices; 20–120 μm penetration | Medium | Medium | |||
| Wax/Paraffin embedding” | BF | 1 μm | High | Medium | High | Connolly (2005), Hamann et al. (2011) |
| Clearing (ClearSee) | CLSM | 0.05 μm optical slices; 250–500 μm penetration | Medium | Medium | High | Kurihara et al. (2015), Richardson and Lichtman (2015) |
| Scanning electron microscopy (SEM) | N/A | Low | High | Medium | Zuberer (1984), Fu et al. (2017), Borisjuk et al. (2018) | |
| X-ray computed microtomography (μCT) | 0.5 μm | Low | High | Low | Dhondt et al. (2010), Pajor et al. (2013), Tracy et al. (2017), Zhao et al. (2019) | |