The largest database of trusted experimental protocols

34 protocols using plan apochromat

1

Quantifying Astrocyte Morphology in Hippocampus

Check if the same lab product or an alternative is used in the 5 most similar protocols
The quantification of the size of astrocytes was done by measuring the volume of astrocytes with a 3D nucleator and the longest diameter of astrocytes in two subregions of hippocampus: CAI.stratum radiatum (CAI.SR) and molecular layer of dentate gyrus (MDG) on GFAP stained sections. Delineation of CAI SR and MDG subregions were performed according to the rat brain atlas (Paxinos and Watson, 2006 ) using a 4 × objective lens (Olympus, Plan Apochromat, N.A. 0.20). Based on the division of granular cell layer of DG (GCL) along the transverse axis into the supra-pyramidal blade (located between the CA3 and CAI areas) and infra-pyramidal blade (located below the CA3 subfield) (Amaral et al., 2007 (link)), MDG was divided into supra-MDG and infra-MDG areas. By using 3D nucleator, the number of half-lines was set at 6 and the mode was vertical uniform random (VI-JR) based on the assumption of rotational symmetry of the astrocytes. Moreover, in this study, we did measure the size of the astrocytes by quantifying the longest diameter of the astrocytes.
Volume and diameter of GFAP-immunopositive astrocytes were estimated with a 100 × oil-immersion objective lens (Olympus, Plan Apochromat, N.A. 1.25) (Fig 1). We sampled randomly 50–80 astrocytes per animal by using optical disector.
+ Open protocol
+ Expand
2

Quantifying Keratinocyte Fluorescence Imaging

Check if the same lab product or an alternative is used in the 5 most similar protocols
Keratinocytes grown on inserts in 12 well plates were washed three times in ice cold PBS and fixed for 45 min in 4% PFA at room temperature. After two washes in PBS, the cells were blocked with 5% goat serum and 5 mg/ml BSA at room temperature for 45 min in PBS with 0.05% Tween 20 (PBST). After blocking, incubation was performed with primary antibodies diluted in PBST with 2.5% goat serum and 5 mg/ml BSA overnight in cold room under rotation. Next day, inserts were washed three times in PBST and incubated with secondary antibodies for 2–4 h at room temperature. The inserts were washed three times and mounted on slides using Prolong Gold antifade reagent mounting medium with DAPI (Invitrogen). Samples were visualized using a Nikon Ti-E microscope (Nikon) inverted fluorescence microscope equipped with Andor Neo/Zyla camera (Andor) and NIS elements advanced research software (Nikon) and a Plan Apochromat objective (Olympus). Fluorescence quantification was done by acquiring several images of each monolayer, covering around 10,000 cells, then analyzed with IntDen measurement (the product of Area and Mean Gray Value) using Fiji (32 (link)). No primary antibody controls are used as a reference for quantification.
+ Open protocol
+ Expand
3

Whole-Brain Imaging using Custom Light-Sheet Microscope

Check if the same lab product or an alternative is used in the 5 most similar protocols
Whole organ imaging was performed with a custom LSM [33 (link)]. The light sheet was generated in digital scanning mode using a galvanometric mirror (6220H, Cambridge Technology, Bedford, MA, USA); confocal detection was achieved by synchronizing the galvo scanner with the line read-out of the sCMOS camera (Orca Flash4.0, Hamamatsu Photonics, Shizuoka, Japan). The laser light was provided by a diode laser (Cobolt, HÜBNER Photonics GmbH, Germany), and an acousto-optic tunable filter (AOTFnC-400.650-TN, AA Opto-Electronic, France) was used to adjust laser intensity. The excitation objective was a 10×, 0.3 NA Plan Fluor from Nikon, while the detection objective was a 10×, 0.6 NA Plan Apochromat from Olympus. The whole brain sample was recorded using a cuvette containing 40% TDE/PBS. The cuvette was mounted on a motorized x-, y-, z-, -stage (M-122.2DD and M-116.DG, Physik Instrumente, Karlsruhe, Germany), which allowed free 3D motion and rotation. Stacks were acquired with a z-step of approximately 3 µm and a xy resolution resulting from the setup configuration of 0.65 µm, with a field of view of 1.3 mm × 1.3 mm. The microscope was controlled via custom-written LabVIEW code (National Instruments, Austin, TX, USA), which coordinated the galvo scanners, the rolling shutter, and the stack acquisition.
+ Open protocol
+ Expand
4

Hippocampal Capillary Diameter Quantification

Check if the same lab product or an alternative is used in the 5 most similar protocols
The capillary diameter was estimated in the molecular layer of the dentate gyrus (MDG), a portion of the hippocampus, which is densely vascularized. The delineation of the MDG was performed on a light microscope by using a 4× objective (Olympus, UPlanSApo, N.A. 0.16) at a magnification of 183×. For analyses of hippocampal vascular diameter, 80–100 capillaries per animal were sampled randomly using an optical disector probe with a height of 20 μm using the newCAST software (Visiopharm, Hørsholm, Denmark). The capillary diameter was determined with a 100× oil-immersion objective lens (Olympus, Plan Apochromat, N.A. 1.25) and the measurement was only performed when the outer wall of the capillary was in focus and fell entirely or partially inside the unbiased counting frame without crossing the exclusion lines of the frame.
+ Open protocol
+ Expand
5

Quantifying AQP4+ Capillary Density in Hippocampus

Check if the same lab product or an alternative is used in the 5 most similar protocols
The length density of AQP4 positive capillaries in the hippocampus was estimated using the global spatial sampling method (Larsen et al., 1998 (link)) with a 60× oil immersion lens (Olympus, Plan Apochromat, N.A. 1.35) on the immunostained sections for AQP4. In a 3D sampling box, isotropic virtual planes with a fixed plane separation distance (d = 25 μm) were systematically and randomly superimposed on the area of interest. The total number of intersections between the virtual planes and the AQP4 positive capillaries was used to estimate the length density of the AQP4 positive capillaries. The height of the counting box was 20 μm with a top guard zone of 5 μm. Based on the size of the counting frame area and the box height, about 200 capillary intersections per animal were counted.
The following formula was applied for measuring the length density of the AQP4 positive capillaries:
where Lv is the length density of the AQP4 positive capillaries; ΣQ is the sum of intersections between the test lines and the capillaries; p(box) is the number of box corners (4); avg a (plane) is the average of the plane area; ΣP is the sum of the box corners hitting the area of interest.
+ Open protocol
+ Expand
6

Imaging and Analysis of Mitochondrial Dynamics

Check if the same lab product or an alternative is used in the 5 most similar protocols
Images (except where noted below) were acquired with an AxioImager M2 (Carl Zeiss) equipped with an Axiocam 506 monochromatic camera (Carl Zeiss) and a 63x oil-immersion objective (Carl Zeiss, Plan Apochromat, NA 1.4), or with an EVOS FL Auto (Thermo Fisher) equipped with an 60x oil-immersion objective (Olympus, Plan Apochromat, NA 1.42). Images in Figure 1 were acquired using an LSM800 (Carl Zeiss) equipped with an Airyscan detector and a 63x oil-immersion objective (Carl Zeiss, Plan Apochromat, NA 1.4). Time-lapse imaging was carried out with an LSM880 (Carl Zeiss) equipped with an Airyscan detector (Carl Zeiss), a 63x oil-immersion objective (Carl Zeiss, Plan Apochromat, NA 1.4), and an environmental chamber set at 30°C (Carl Zeiss). Images were acquired with ZEN software (Carl Zeiss) or EVOS software (Thermo Fisher) and processed with Fiji (Schindelin et al., 2012 (link)). Image panels depicting mitochondrial morphology were individually contrast enhanced, while all others where processed identically.
+ Open protocol
+ Expand
7

Fluorescence In Situ Hybridization of 18S rRNA

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells grown on glass cover slips were fixed with 4% paraformaldehyde in PBS for 15 min. After washing in PBS, the cells were permeabilized in 70% ethanol overnight at 4°C. They were then re-hydrated twice for 5 min in 2× SSC containing 10% formamide. The precursors to the 18S rRNA were localized by fluorescence in situ hybridization (FISH) with a 5′ ITS1 probe coupled to Cy3 (35 (link)). The cover slips were washed in 2× SSC containing 10% formamide, and DNA was counter stained with Hoechst 33342 (Invitrogen), before mounting in Mowiol 4.88 (PolyScience, Inc.). The slides were observed with an inverted microscope (IX-81; Olympus), equipped with a ×100, oil immersion objective (Plan Apochromat, 1.4 NA; Olympus) and an Orca Flash 4.0 camera with a pixel size of 6.5 μm (Hamamatsu), driven by MetaMorph (MDS Analytical Technologies).
+ Open protocol
+ Expand
8

Immunofluorescence Imaging of Chondrocytes

Check if the same lab product or an alternative is used in the 5 most similar protocols
Porcine articular chondrocytes were cultured on glass coverslips, fixed with 4% paraformaldehyde at 4 °C for 15 min, permeabilized with 2% Triton X-100, and blocked with 5% donkey or goat serum for 30 min. Then, cells were exposed to primary antibodies at 4 °C overnight and then to fluorescent secondary antibody. Immunolabeling was visualized using a Zeiss 780 confocal microscope. Anti-PIEZO1 (NBP1-78537, Novus) was used. Chondrocytes were also labeled with fluorescent Phalloidin (phalloidin-CF568, Biotium) to visualize F-actin or with BT7R-dylight488 (Thermo Fisher) to visualize β-tubulin and then imaged. A Zeiss 780 confocal microscope (Plan Apochromat 40×/1.4 NA oil immersion objective) or a BX61 Olympus upright microscope (X-Apochromat 40×/1.4 NA oil immersion objective) equipped with high-resolution charge-coupled device (CCD) camera and ISEE software (ISEE Imaging Systems) were used. For confocal laser scanning microscopy, confocal slices or z-stacks were acquired following refs. 56 (link) and 57 (link).
Circular chondrocytes were selected as region-of-interest (ROI), and their ROI integrated density was determined using ImageJ, subtracted for noncellular background in immunocytochemistry applications, yielding individual metric data points per cell, see also SI Appendix, Fig. S1.
+ Open protocol
+ Expand
9

Imaging Cells with DeltaVision Microscope

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells were imaged on a DeltaVision microscope (Applied Precision) using either a 60× 1.3 NA Plan-Apochromat or a 40× 1.3NA UPlan-FL N objective lens (Olympus). z-stacks were acquired with a CoolSNAP HQ camera (Photometrics) and SoftWoRx acquisition software (Applied Precision). Images were deconvolved using Deltavision SoftWoRx software and objective specific point spread function. Projections of three z-stacks were made using FIJI.
+ Open protocol
+ Expand
10

Immunofluorescence Staining Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells were fixed for 15 min at room temperature in a 4 % (w/v) PFA, 4 % (w/v) sucrose, 20 mM NaOH and 5 mM MgCl2 in PBS, pH 7.4. Cells were permeabilized and blocked for 30–60 min at room temperature in 15 % (w/v) goat serum, 0.3 % (v/v) Triton X-100, 450 mM NaCl, 20 mM phosphate buffer, pH 7.4 and incubated at 4 °C overnight with primary antibodies diluted in blocking buffer. Coverslips were mounted onto slides with PBS containing 70 % glycerol and 1 μM DAPI. Representative images were taken using a confocal microscope Fluoview FV1000 Olympus IX81 (Center Valley, PA, USA) with an oil immersion objective (×40 or × 60 × 1.4 NA Plan-Apochromat; Olympus) using laser excitation at 405, 488 or 594 nm, and processed using Fiji [91 (link)]. Alternatively bEnd.3 cells were stained with Diff Quick (Dade Behering, BioMap) and acquired with inverted microscope Olympus IX53 (Center Valley, PA, USA).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!