Journal: STAR Protocols

Article Title: Protocol for 3D-guided sectioning and deep cell phenotyping via light sheet imaging and 2D spatial multiplexing

doi: 10.1016/j.xpro.2025.104296

Figure Lengend Snippet: 3D spatial and data analysis workflow 3D spatial analysis of 3D-IF stained and optically cleared samples with UltraMicroscope Blaze™ light sheet microscope (Step 16). Post processing (stitching) in case data was acquired with tile-scanning (Step 18). Surfaces generation of autofluorescence and target region with Imaris software (Oxford Instruments) and target plane definition with “Oblique Slicer” tool (Step 20 and 20).

Article Snippet: Continue the workflow in Imaris to create orientation marks for further analysis.

Techniques: Staining, Microscopy, Software

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Molecular assemblies and pharmacology of cerebellar GABA A receptors

doi: 10.1073/pnas.2524504123

Figure Lengend Snippet: α1-containing cerebellar GABA A Rs show distinct α and β subunit combinations. Cryo-EM data analysis of the PZ-II-029/GABA dataset identifies five distinct receptor assemblies. ( A ) Two predominant assemblies with well-defined subunit identity, β2-α1-β2-α1-γ2 (viewed from the extracellular space, subunits counted counter-clockwise) and β2-α1-β1-α6-γ2. ( B ) Additional assemblies showing ambiguous density at one or both β subunit positions, corresponding to β2-α1-β2/3-α1-γ2, β1-α1-β1/2-α1-γ2, β1/2-α1-β2/3-α1-γ2. When two subunits are listed at one position, the first one denotes the predominant identity. Percentages of each receptor assembly are calculated based on the number of final particles used for the cryo-EM reconstruction ( SI Appendix , Fig. S5 ). The extracellular domain (ECD) is colored based on the subunit identity. All N -glycosylation is colored in teal, and representative glycosylation at the ECD periphery is labeled with an arrow.

Article Snippet: In data analysis for both datasets ( SI Appendix , Figs. S3–S5 ), more than 2 million GABA A R particles exhibiting salient receptor features in 2D class averages are obtained following a simple cryo-EM cleanup workflow ( SI Appendix , Figs. S3 A and S5 A ).

Techniques: Cryo-EM Sample Prep, Glycoproteomics, Labeling