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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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qiaseq mirna primary quantification processing workflow  (Qiagen)
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Schematic overview of the <t>workflow</t> for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending <t>on</t> <t>spheroid</t> size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.
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Schematic overview of the workflow for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending on spheroid size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.

Journal: Scientific Reports

Article Title: Contribution of tissue clearing and 3D image analysis to in vitro modeling of human cortical development

doi: 10.1038/s41598-026-41741-7

Figure Lengend Snippet: Schematic overview of the workflow for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending on spheroid size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section. Illustrations were created with BioRender.

Article Snippet: Fig. 1 Schematic overview of the workflow for 2D and 3D analysis of hiPSC-derived neurospheres. (A) Generation of neurospheres from hiPSC, followed by fixation and preparation for either 2D cryosectioning or 3D tissue clearing. (B) Cleared neurospheres are embedded in agarose for light-sheet fluorescence microscopy, producing a Z-stack of ~ 300–500 optical sections at 3 μm intervals, depending on spheroid size and maturation. (C) Quantification workflow in Imaris using the spot detection function to enumerate positive cells across the entire spheroid, providing precise volumetric data rather than estimates from a single section.

Techniques: Derivative Assay, Fluorescence, Microscopy