Journal: STAR Protocols

Article Title: Protocol to study synapse density or volume—SynDOVE—in brain using confocal microscopy and Imaris three-dimensional surface rendering software

doi: 10.1016/j.xpro.2026.104465

Figure Lengend Snippet: Conversion of ND2 files to IMS files Double-click image to automatically convert files to.ims format for Imaris. ND2 files will have the white 3D box and right-pointing arrow icons in the lower left corner. IMS files will have the 3D box icon in the lower left corner.

Article Snippet: • Below is a table ( ) that summarizes the recommended minimum image acquisition parameters for puncta detection and surface segmentation during 3D surface rendering in Imaris.

Techniques:

Journal: bioRxiv

Article Title: Sphingosine-1-Phosphate Receptor 1 regulates competition dependent astrocyte morphogenesis and tiling in murine cortex

doi: 10.64898/2026.03.28.714989

Figure Lengend Snippet: ( A ) S1PR1 ΔAST or littermate controls were intracranially injected with the adenoassociated virus (AAV), pZac2.1-GfaABC1D-YFP, to sparsely label astrocytes. Sparsely labeled astrocytes from L2-3 somatosensory cortices were imaged and analyzed. ( B ) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from S1PR1 ΔAST or littermate controls at P30. (C) Quantification of astrocyte volume (left), and soma volume (right) from surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume (left), astrocyte process/filament length (middle) and area (right) from filament traces generated using IMARIS. ( E ) Plot depicting the proportion of astrocyte filament thicknesses grouped by mean diameter and represented as % of total filaments. ( F ) Sholl analyses of IMARIS rendered filament traces of astrocytes from S1PR1 ΔAST and littermate controls. Data represents the mean ± SEM from total 26 and 25 astrocytes from n=5 mice per group. * = p <0.05, *** = p <0.001, ns=non-significant, Unpaired Welch’s T-test.

Article Snippet: Sparsely labeled astrocytes were imaged from both upper and deeper somatosensory cortex from P30 pups. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from control or Cre expressing littermates at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume from filament traces generated using IMARIS. ( E ) Sholl analyses of IMARIS rendered filament traces of astrocytes from Cre.P2A.YFP and YFP only.

Techniques: Injection, Virus, Labeling, Generated

Journal: bioRxiv

Article Title: Sphingosine-1-Phosphate Receptor 1 regulates competition dependent astrocyte morphogenesis and tiling in murine cortex

doi: 10.64898/2026.03.28.714989

Figure Lengend Snippet: ( A ) Sparsely YFP-labeled L4-5 somatosensory cortical astrocytes were imaged and analyzed. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from S1PR1 ΔAST or littermate controls at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume (left), astrocyte process/filament length (middle) and area (right) from filament traces generated using IMARIS. ( E ) Plot depicting the proportion of astrocyte filaments grouped at various mean diameter and represented as % of total filaments revealed no differences in mean dendrites in S1PR1 ΔAST astrocytes. ( F ) Sholl analyses of IMARIS rendered filament traces of astrocytes from S1PR1 ΔAST and littermate controls. Data represents the mean ± SEM of 24 and 22 astrocytes from n=5 mice per group. * = p <0.05, ** = p <0.01, ns=non-significant, Unpaired Welch’s T-test.

Article Snippet: Sparsely labeled astrocytes were imaged from both upper and deeper somatosensory cortex from P30 pups. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from control or Cre expressing littermates at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume from filament traces generated using IMARIS. ( E ) Sholl analyses of IMARIS rendered filament traces of astrocytes from Cre.P2A.YFP and YFP only.

Techniques: Labeling, Generated

Journal: bioRxiv

Article Title: Sphingosine-1-Phosphate Receptor 1 regulates competition dependent astrocyte morphogenesis and tiling in murine cortex

doi: 10.64898/2026.03.28.714989

Figure Lengend Snippet: (A) Schematics showing S1PR1 deletion in sparse astrocytes by delivering AAV-GfaABC1D-YFP-P2A-Cre or AAV-GfaABC1D-YFP control in S1PR1 fl/fl mouse pups. (B) Sparsely labeled astrocytes were imaged from L2-3 somatosensory cortex from P30 pups. ( C ) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from S1PR1 ΔAST or littermate controls at P30. (D) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated by IMARIS. ( E ) Quantification of astrocyte territory volume (left) filament length (middle) and filament area (right) from filament traces generated by IMARIS. (F) Plot depicting the proportion of astrocyte filaments grouped by various mean diameter and represented as % of total filaments revealed no differences in mean dendrites in S1PR1 ΔAST astrocytes. ( G ) Sholl analyses of IMARIS rendered filament traces of YFP labeled sparse astrocytes from S1PR1 ΔAST and littermate controls. Data represents the mean ± SEM of 23 and 24 astrocytes from n=4 mice per group. * = p <0.05, ** = p <0.01, ns=non-significant, Unpaired Welch’s T-test.

Article Snippet: Sparsely labeled astrocytes were imaged from both upper and deeper somatosensory cortex from P30 pups. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from control or Cre expressing littermates at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume from filament traces generated using IMARIS. ( E ) Sholl analyses of IMARIS rendered filament traces of astrocytes from Cre.P2A.YFP and YFP only.

Techniques: Control, Labeling, Generated

Journal: bioRxiv

Article Title: Sphingosine-1-Phosphate Receptor 1 regulates competition dependent astrocyte morphogenesis and tiling in murine cortex

doi: 10.64898/2026.03.28.714989

Figure Lengend Snippet: (A) Schematics showing S1PR1 deletion in sparse astrocytes by delivering AAV-GfaABC1D-YFP-P2A-Cre or AAV-GfaABC1D-YFP control in S1PR1 fl/fl mouse pups. Sparsely labeled astrocytes were imaged from L4-5 somatosensory cortex from P30 pups. ( B ) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from S1PR1 ΔAST or littermate controls at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated by IMARIS. ( E ) Quantification of astrocyte territory volume (left) process/filament length (middle) and area (left) from filament traces generated by IMARIS. (F) Plot depicting the proportion of astrocyte filaments grouped by mean diameter and represented as % of total filaments revealed no differences in mean dendrites in S1PR1 ΔAST astrocytes. ( G ) Sholl analyses of IMARIS rendered filament traces of GFP labeled sparse astrocytes from S1PR1 ΔAST and littermate controls. Data represents the mean ± SEM of 22 and 17 astrocytes from n=4 mice per group. * = p <0.05, ** = p <0.01, *** = p <0.001 ns=non-significant, Unpaired Welch’s T-test.

Article Snippet: Sparsely labeled astrocytes were imaged from both upper and deeper somatosensory cortex from P30 pups. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from control or Cre expressing littermates at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume from filament traces generated using IMARIS. ( E ) Sholl analyses of IMARIS rendered filament traces of astrocytes from Cre.P2A.YFP and YFP only.

Techniques: Control, Labeling, Generated

Journal: bioRxiv

Article Title: Sphingosine-1-Phosphate Receptor 1 regulates competition dependent astrocyte morphogenesis and tiling in murine cortex

doi: 10.64898/2026.03.28.714989

Figure Lengend Snippet: B) Schematics showing S1PR1 deletion in neighboring astrocytes in two-color schemes by delivering AAV-GfaABC1D-YFP-P2A-Cre plus AAV-GfaABC1D-tdTomato-P2A-Cre or AAV-GfaABC1D-YFP plus AAV-GfaABC1D-tdTomato controls in S1PR1 fl/fl mouse pups. ( C ) Example 20x confocal image to show the labelling by two color viruses. (D) Representative confocal images and subsequent IMARIS 3D surface/filament renderings to create territories of neighboring astrocytes from KO:KO or littermate WT:WT controls at P30. (E) Quantification of astrocyte territory overlap volume represented as % of total volume from two neighboring astrocytes. Data represents the mean ± SEM of 23 and 18 pairs of neighboring astrocytes from n=3 and 4 mice per group. **** = p <0.0001, Unpaired Welch’s T-test.

Article Snippet: Sparsely labeled astrocytes were imaged from both upper and deeper somatosensory cortex from P30 pups. (B) Representative confocal images and subsequent IMARIS 3D surface/filament renderings of YFP astrocytes from control or Cre expressing littermates at P30. (C) Quantification of astrocyte volume (left) and soma volume (right) from Surface renderings generated using IMARIS. ( D ) Quantification of astrocyte territory volume from filament traces generated using IMARIS. ( E ) Sholl analyses of IMARIS rendered filament traces of astrocytes from Cre.P2A.YFP and YFP only.

Techniques: