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Figure 7. Surface and spot reconstruction (Questions 2 and 3) (A) <t>GluR1</t> signal alone (green). (B) Filtered surface reconstruction of GluR1 signal. (C) Filtered spot reconstruction of GluR1 signal (red) merged with GluR1 signal (green). (D) Surface and spot reconstructions merged with GluR1 signal. For all images, scale bar = 0.3 mm.
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Image Search Results


Figure 7. Surface and spot reconstruction (Questions 2 and 3) (A) GluR1 signal alone (green). (B) Filtered surface reconstruction of GluR1 signal. (C) Filtered spot reconstruction of GluR1 signal (red) merged with GluR1 signal (green). (D) Surface and spot reconstructions merged with GluR1 signal. For all images, scale bar = 0.3 mm.

Journal: STAR protocols

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.

doi: 10.1016/j.xpro.2023.102707

Figure Lengend Snippet: Figure 7. Surface and spot reconstruction (Questions 2 and 3) (A) GluR1 signal alone (green). (B) Filtered surface reconstruction of GluR1 signal. (C) Filtered spot reconstruction of GluR1 signal (red) merged with GluR1 signal (green). (D) Surface and spot reconstructions merged with GluR1 signal. For all images, scale bar = 0.3 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Techniques:

Figure 8. Dendritic spot and surface filtering (Questions 2 and 3) (A) Dendrite reconstruction (blue/gray) with filtered GluR1 spots reconstruction (red). (B) Results of Spots Close to Filament Border XTension: farther than threshold (blue) and closer than threshold (red). (C) Spots closer than the ‘‘dendritic’’ threshold isolated. D) Dendritic spots with dendritic surfaces. Scale bar = 1 mm.

Journal: STAR protocols

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.

doi: 10.1016/j.xpro.2023.102707

Figure Lengend Snippet: Figure 8. Dendritic spot and surface filtering (Questions 2 and 3) (A) Dendrite reconstruction (blue/gray) with filtered GluR1 spots reconstruction (red). (B) Results of Spots Close to Filament Border XTension: farther than threshold (blue) and closer than threshold (red). (C) Spots closer than the ‘‘dendritic’’ threshold isolated. D) Dendritic spots with dendritic surfaces. Scale bar = 1 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Techniques: Isolation

Journal: STAR Protocols

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices

doi: 10.1016/j.xpro.2023.102707

Figure Lengend Snippet:

Article Snippet: Anti-GluR1 (mouse) (dilution: 1:250) , Novus Biologicals , NBP2_22399.

Techniques: Recombinant, Saline, Plasmid Preparation, Software, Microscopy