Cell Mapping | Pinpoint the spatial location of specific cell types within tissues and organoids

Cell Mapping

Use Case: Pinpoint the spatial location of specific cell types within tissues and organoids

Anatomical insights
from tissue micro-environment:

Quantitatively measure
pathophysiological
progression:

Accurate and
versatile spatial
mapping:

Use transgenic expression or immunolabeling of cell-specific markers to readily identify distinct cell-types within their native tissue environment.

Use quantitative analysis on the spatial position of single cells to measure multi-scale features that characterize the microenvironment, cytoarchitecture, whole organoid/tissue.
Quantitate the extent of cellular infiltration within diseased, damaged, and inflamed areas.

Volumetric Imaging of a d59 human fetal eye after whole mount staining and clearing:

Figure 1D (left) extracted from  Wohlschlegel et al. (2023): 

  • (Top) A 2D sub-stack (20/1,370) with maximum intensity projection of the fetal eye immunolabeled with IBA1 (green), RCVRN (magenta), and RLBP1 (red). Inset shows some RLBP1+ cells in the RPE and in the retina.

Digital Slicing of Cleared Newborn PV-Ai9 Mouse Revealing Detailed Structures

Figure 3 from Nudell et al. (2022) Nature Methods presents a schematic of digital slicing planes used to collect images of a cleared newborn PV-Ai9 mouse, showing detailed structures in various regions, including the cochlea, spinal cord, abdominal organs, and pulmonary vasculature, with corresponding equivalent structures in SST-Ai9 mice.

Brain-wide Mapping of MC3R Neurons Using 3D Rendering and Allen CCF Registration​

Figure 2 from Bedenbaugh et al. (2022) Journal of Comparative Neurology depicts a brain-wide mapping of melanocortin-3 receptor (MC3R) neurons using 3D rendering and coronal views, highlighting MC3R labeling in various brain regions, with cell density quantified by registering cell locations to the Allen Common Coordinate Reference Framework. 

For additional publications supporting this use case refer to:

  • Folorunso et al. (2023) Science Reports
  • Paulsen et al. (2022) Nature: Supplemental Figure 4A,B. a, Immunohistochemistry of Mito210 SUV420H1+/− and control organoids cultured for one month (35 d.i.v.). Optical section from the middle of whole-organoid dataset. Scale bars are 500 μm. SOX2, a marker of neuronal progenitors, is shown in red, and nuclei (Syto16) are shown in blue. b, Immunohistochemistry for the postmitotic excitatory neuronal marker TBR1 and GABAergic marker DLX2 in Mito294 control and SUV420H1+/− organoids at one month (35 d.i.v.). Scale bars: 200 μm.
  • Sweeney et al. (2022) Science Translational Medicine
  • Knights et al. (2021) Embo Journal: Figure 1A shows 3D imaging of WT and ChAT-eGFP IWAT (subcutaneous inguinal fat pad) using the Adipo-Clear method (Chi et al, 2018) and light sheet microscopy. 
  • Albanese et al. (2020) Scientific Reports:  Figures (a) Schematic shows cerebral organoids grown from stem cells, fixed with SHIELD, delipidated, stained via eFLASH, and imaged with light-sheet microscopy. Quantitative analysis uses algorithms and neural networks to measure multiscale features for high-dimensional phenotyping.(b) SHIELD is compatible with common markers for cerebral organoids.(c) Organoids, after delipidation and dPROTOS treatment, become optically transparent for confocal microscopy. (d) SHIELD preserves fluorescence, mRNA, and protein epitopes. (e) 3D and 2D renderings of cerebral organoids with multicolor staining (nuclei, neurons, glial cells).
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