For the quantification of TH‐positive (TH+) neurons in SNpc, 3 brains from adult mice were collected 2 m.p.i., while Cavalieri estimator was used to estimate volume SNpc in both hemispheres. Brain sections outlines were carried out using a Zeiss fluorescent microscope (Imager.M2, ZEISS, Oberkochen, Germany) fully motorized and interfacing with a Dell computer running StereoInvestigator® (MBF Bioscience, Williston, Vermont, USA). SNpc cells labeled with corresponding markers were quantified in 8 serial coronal sections spaced 150 µm apart (section interval = 3), spanning the entire brain hemisphere. Outline and fiduciary marks were drawn at 2.5x magnification (EC‐Plan‐NEOFLUAR 2.5X/0.075, ZEISS, Oberkochen, Germany) to delineate reference points. Limits for areas of interest were drawn following a mouse brain atlas [23 ]. Cell counting was done blinded to genotype and treatment, at 63x magnification (Plan/APOCHROMAT 63X/1.4 Oil DIC, ZEISS, Oberkochen, Germany) using a 3D counting frame. See Table 1 for the parameters of stereological counting.
Plan apochromat 63x 1.4 oil dic
Manufactured by Zeiss
Sourced in Germany
The Plan-Apochromat 63x/1.4 Oil DIC is a high-numerical aperture objective lens designed for microscopy applications. It features a magnification of 63x and a numerical aperture of 1.4, which provides a high resolution and a shallow depth of field. The lens is optimized for use with oil immersion, and it incorporates Differential Interference Contrast (DIC) optics for enhanced contrast and detail visualization.
Automatically generated - may contain errors
Lab products found in correlation
Ec plan neofluar 2 5x 0, by Zeiss (2 mentions)
Imager m2, by Zeiss (2 mentions)
Stereoinvestigator, by MBF Biosciences (2 mentions)
Ec plan neofluar 40x 0, by Zeiss (2 mentions)
Lumar v12, by Zeiss (2 mentions)
Axiocam mr, by Zeiss (2 mentions)
Ec plan neofluar 20x 0, by Zeiss (2 mentions)
Ec plan neofluar 10x 0, by Zeiss (2 mentions)
Axio observer z1 inverted microscope, by Zeiss (2 mentions)
Axio imager z1, by Zeiss (2 mentions)
Axio zoom v16, by Zeiss (2 mentions)
Lsm 880 confocal microscope, by Zeiss (2 mentions)
Lsm 510 microscope, by Zeiss (1 mentions)
Anti flag m2 antibody, by Merck Group (1 mentions)
Paraformaldehyde (pfa), by Electron Microscopy Sciences (1 mentions)
Live dead baclight bacterial viability kit, by Thermo Fisher Scientific (1 mentions)
Lsm 510 meta, by Zeiss (1 mentions)
Phosphate buffered saline (pbs), by Harvard Bioscience (1 mentions)
4 6 diamidino 2 phenylindole (dapi), by Merck Group (1 mentions)
Axiovision 4, by Zeiss (1 mentions)
14 protocols using plan apochromat 63x 1.4 oil dic
1
Quantification of Dopaminergic Neurons in Mouse SNpc
2
Imaging of Surface Na⁺V1.5 Expression
3
Bacterial Viability Assessment using Fluorescent Stains
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Fluorescent propidium iodide (PI) stain was used with the SYTO® 9 (Live/Dead® BacLight™ Bacterial Viability Kit, Life Technologies GmbH, Darmstadt, Germany) to determine the number of viable and dead bacterial cells [53 (link)]. Intact cells and those with disrupted membranes can be penetrated by the green fluorescence stain SYTO® 9, whereas the red-fluorescent PI can only penetrate disrupted cell membranes. Hence, viable and active bacterial cells fluoresce green and non-intact cells fluoresce red. The PI and SYTO® 9 were diluted in 0.9% NaCl to achieve a final concentration of 0.1 nmol/mL. The different materials covered with the initial bacterial adhesion were then transferred to multiwell plates and stained with 1 mL SYTO® 9/PI solution in 0.9% NaCl per well, for 15 min at room temperature, in a dark chamber. The stained materials were subsequently placed with the contaminated side on a drop of 0.9% NaCl solution in an 8-chambered cover glass (µ Slide 8 well, ibidi GmbH, Munich, Germany), and analyzed using an inverse epifluorescence microscope (ApoTome.2, Axio Observer.Z1, ZEISS, Oberkochen, Germany) with a 63 × oil immersion objective (Plan-Apochromat 63x/1.4 Oil DIC, ZEISS, Oberkochen, Germany).
4
Cellular Internalization of Protein Particles
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J744 cells were grown on microscope coverslips to semiconfluent state and were washed by RPMI-1640, pH 7.3. Particles containing 2.5 μg of protein and cell nuclear dye Hoechst 33342 in 1 mL RPMI-1640 were incubated with cells for 15 min at 4°С and for 60 min at 37°С. Non-bound proteins were washed twice by RPMI-1640. After incubation, J774 cells were fixed by 4% solution of paraformaldehyde in 0.1 M phosphate buffer for 40 min at 4°С. Coverslips with cells were mounted on a slide in mounting medium based on polyvinyl alcohol. Cell specimens were analyzed with confocal microscope Zeiss LSM 510 Meta (Carl Zeiss, Jena, Germany) with oil immersion objective Plan-Apochromat 63x/1.4 Oil DIC.
5
Quantifying Adherent Microbiome on Dental Materials
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The root-filling materials and the control material were stained after the initial in situ adhesion with DAPI which visualizes all adherent microorganisms under the epifluorescence microscope. A stock solution of DAPI (1 mM) was prepared in a phosphate-buffered NaCl solution (PBS, Biochrom GmbH, Berlin, Germany). The staining solution consisted of 6 µl of the stock solution, which was diluted in 12 mL PBS. The material samples were incubated with 1 mL DAPI (Merck, Darmstadt, Germany) and the staining was conducted in a dark chamber for 10 min. Afterward, the DAPI solution was removed by rinsing with PBS and dried at room temperature. To quantify the total bacterial number per cm2, the same procedure was conducted using the inverse epifluorescence microscope (ApoTome.2, Axio Observer.Z1, ZEISS, Oberkochen, Germany) with a 63 × oil immersion objective (Plan-Apochromat 63x/1.4 Oil DIC, ZEISS, Oberkochen, Germany) as described above for the determination of viable and dead bacteria using live/dead staining.
6
Microscopic imaging of fixed cells
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For all the microscopy experiments cells were fixed using methanol, stained with DAPI, imaged by a microscope (Axio Imager 2; Carl Zeiss) with a 63x objective (Plan-APOCHROMAT, 63x/1.4 Oil DIC; Carl Zeiss), and processed with Axio Vision 4.8 software (Carl Zeiss). A Z-stack of ∼2 μm thickness, with single planes spaced by 0.3 μm, was acquired and maximum intensity projections were generated. To compare signal intensities, all images were taken with the same exposure conditions and processed similarly.
7
Microscopy of Drechmeria coniospora spore germination and hyphal growth
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For microscopy around 4x104 spores were inoculated on thin LNA and incubated for at least 14 h at 28°C. Conventional fluorescence images were captured at room temperature using a Zeiss Plan-Apochromat 63x/1.4 Oil DIC, EC Plan-Neofluar 40x/0.75, EC Plan-Neofluar 20x/0.50, or EC Plan-Neofluar 10x/0.30 objective attached to a Zeiss AxioImager Z.1 and AxioCamMR. Color images were acquired using the AxioCam 105 color. Images were collected using ZEN 2012 Blue Edition.
Confocal images were captured at room temperature using a Leica HCX PL APO 63x1.4 oil objective attached to a Leica TC SP5 and conventional photomultiplier tube detectors (Leica, Wetzlar, Germany). Kryo-SEM was performed as previously described [72 (link)]. Stereomicroscopy was performed using a Zeiss Lumar.V12 with AxioCam HRc and NeoLumar S 1.5x objective. Images were collected using the AxioVision software.
To quantify germination time and hyphal growth of D. flagrans wild-type and the ΔsofT strain an AxioObserver Z1 inverted microscope employing a 10x/0.30 N.A. objective (Zeiss) was used.
Confocal images were captured at room temperature using a Leica HCX PL APO 63x1.4 oil objective attached to a Leica TC SP5 and conventional photomultiplier tube detectors (Leica, Wetzlar, Germany). Kryo-SEM was performed as previously described [72 (link)]. Stereomicroscopy was performed using a Zeiss Lumar.V12 with AxioCam HRc and NeoLumar S 1.5x objective. Images were collected using the AxioVision software.
To quantify germination time and hyphal growth of D. flagrans wild-type and the ΔsofT strain an AxioObserver Z1 inverted microscope employing a 10x/0.30 N.A. objective (Zeiss) was used.
8
In vivo Imaging of C. elegans Cilia
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In vivo imaging was performed as described recently21 (link). Worms were imaged on a 4% agarose pad containing 30 mM sodium azide using an Axio imager M1(Carl Zeiss Microscopy GmbH, Jena, Germany) equipped with Axiocam 503mono and Zeiss2.3 pro software (Carl Zeiss Microscopy GmbH). When worms were imaged on plates, the plates were precooled on ice for 5 min to immobilise the worms and imaged using Leica M165FC equipped with Leica DFC340FX camera and Leica application Suite 3.3.1 software or Axiozoom V16, (Carl Zeiss Microscopy GmbH) equipped with Axiocam 506mono and Zeiss 2.3 software (Carl Zeiss Microscopy GmbH).
For confocal imaging of ciliary structures, day 1 adult hermaphrodites were cultured at 22 °C and immobilised with 25 mM levamisole on a 3% agarose pad. Worms were imaged using LSM980 Airyscan 2 equipped with Plan-Apochromat 63x /1.4 oil DIC and ZEN Connect Modul (Carl Zeiss Microscopy GmbH). The presence of the dyf-1(mn335) mutation was confirmed by DiI staining. Image J was used for image processing and analysis.
For confocal imaging of ciliary structures, day 1 adult hermaphrodites were cultured at 22 °C and immobilised with 25 mM levamisole on a 3% agarose pad. Worms were imaged using LSM980 Airyscan 2 equipped with Plan-Apochromat 63x /1.4 oil DIC and ZEN Connect Modul (Carl Zeiss Microscopy GmbH). The presence of the dyf-1(mn335) mutation was confirmed by DiI staining. Image J was used for image processing and analysis.
9
Confocal and Structured Illumination Microscopy
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Confocal images were acquired using LSM880 confocal microscope (Carl Zeiss) with 40x/1.2 lens objective. For all centrosome counting experiments, whole cell depth was covered by z-stack imaging method. Z-stack images were then combined by “maximum intensity projection” analysis method in “Zen 2.6 blue edition” (Carl Zeiss) software. For ID1 intensity analysis, each centriole was firstly masked and ID1 intensity within the masked regions was measured. This signal was then normalized by the size of the centriole.
Structural illumination images were acquired using a Zeiss ELYRA S.1 microscope (Carl Zeiss) with Plan-Apochromat 63x/1.4 Oil DIC. Green (488 nm) and Red (561 nm) channels were acquired by sequentially alternating the excitation whilst retaining the same setting with respect to phase, rotation, and multi-cube filterset. Images were acquired with five phases, five rotations. Green channel signal was acquired with a grating of 28.0 μm and red was 34.0 μm. Images were processed using the automatic reconstruction settings in the Zen software.
Structural illumination images were acquired using a Zeiss ELYRA S.1 microscope (Carl Zeiss) with Plan-Apochromat 63x/1.4 Oil DIC. Green (488 nm) and Red (561 nm) channels were acquired by sequentially alternating the excitation whilst retaining the same setting with respect to phase, rotation, and multi-cube filterset. Images were acquired with five phases, five rotations. Green channel signal was acquired with a grating of 28.0 μm and red was 34.0 μm. Images were processed using the automatic reconstruction settings in the Zen software.
10
Microscopic Fungal Spore Analyses
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For microscopical analyses 4x104 spores were inoculated on thin LNA slides and incubated for at least 12 h at 28°C. Conventional fluorescence images were captured at room temperature using a Zeiss Plan-Apochromat 63x/1.4 Oil DIC, EC Plan-Neofluar 40x/0.75, EC Plan-Neofluar 20x/0.50, or EC Plan-Neofluar 10x/0.30 objective with a Zeiss AxioImager Z.1 and AxioCamMR. For Confocal microscopy, the Zeiss LSM 900 with Airyscan 2 was used. Images were collected using ZEN 2012 Blue Edition.
Stereomicroscopy was performed using a Zeiss Lumar.V12 with AxioCam HRc and NeoLumar S 1.5x objective. Images were collected with the AxioVision software.
For the long-term observation virulence assay of D. flagrans wild-type and the ΔcyrA strain an AxioObserver Z1 inverted microscope employing a 10x/0.30 N.A. objective (Zeiss) was used.
The fungal cell wall was visualized by Calcofluor-white (CFW, fluorescent brightener 28, Sigma Aldrich) as described [15 (link)].
Stereomicroscopy was performed using a Zeiss Lumar.V12 with AxioCam HRc and NeoLumar S 1.5x objective. Images were collected with the AxioVision software.
For the long-term observation virulence assay of D. flagrans wild-type and the ΔcyrA strain an AxioObserver Z1 inverted microscope employing a 10x/0.30 N.A. objective (Zeiss) was used.
The fungal cell wall was visualized by Calcofluor-white (CFW, fluorescent brightener 28, Sigma Aldrich) as described [15 (link)].
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