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1 225 protocols using axio observer

1

Characterizing Spheroid Morphology and Function

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Photographs of spheroids cultured for 4 days in the pyramid-shaped microwells were obtained using a fluorescence microscope (bright field, Zeiss Axio Observer; Zeiss). The characterization of spheroids shape (diameter, circularity, and aspect ratio) was performed setting first the scale (pixel to μm conversion) using ImageJ (FIJI). A Gaussian filter has been used to blur the image facilitating the spheroids edges detection (typical sigma radius between 3–7). The image has been then converted to a mask. Finally, parameters can be obtained using Analyze Particles. Immunofluorescence microscopy was conducted using a confocal microscope (LSM880; Zeiss) or fluorescence microscope (Zeiss Axio Observer; Zeiss). ImageJ was also used for the quantification of images collected from both fluorescence and confocal microscopes. Spheroids were imaged for each condition and their fluorescence intensities were used to compare the expression of ROS or AdipoRed dye. Specifically, background intensities of raw fluorescence images were subtracted, and intensities from multiple regions in each spheroid were averaged to compare with others. Intensities from spheroids with the FFAs induction were normalized by those from spheroids without the supplement.
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Tumor Cell Adhesion Dynamics on HUVECs

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For images in 2D, 1 × 105 tumor cells were plated on 12 well plates and the day after treated with either 100 μg/ml LDL or the same volume of control (150 mM NaCl, 0.01% EDTA) for 6 h. After that, cells were trypsinized and 0.5 × 104 cells were plated on top of confluent monolayers of HUVECs, that had been plated the day before at 2 × 104 cells per well on top of 0.2% gelatin (8 well 1 cm2 area ibidi plates). Cells were imaged on a Zeiss Axio Observer under controlled CO2 and temperature. Pictures were taken every 5 min at both transmitted (green channel) and reflected light using a Zeiss Axio Observer under controlled CO2 and temperature.
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Quantifying Platelet Adhesion and Aggregation

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In vitro flow studies were performed on multichannel microfluidic capillary systems which had been coated with either 300 µg/ml fibrinogen or 25 μg/ml collagen overnight at 4 °C and then blocked with 5% BSA (5 mg/ml) for 1 hour. Whole blood from healthy donors was obtained in PPACK (50 µM) and platelets were fluorescently labelled with 3,3′-Dihexyloxacarbocyanine Iodide (10 µM) prior to being flowed for 2 minutes at a shear rate of 1000 s−1 (37 °C). Following this initial flow to adhere platelets and form aggregates, buffer only or GSNO (100 nM) were post-flowed over the adhered platelets for a further 20 minutes prior to fixation with 4% paraformaldehyde. Fixed adhered platelets were either restained overnight with 3,3′-Dihexyloxacarbocyanine Iodide (10 µM) or permabilised in 0.1% Triton X-100 and stained with FITC-phalloidin before imaging using the Zeiss Axio Observer (x63 oil immersion objective, 1.4 NA (Zeiss, Cambridge, UK)). Acquired images were analysed using ImageJ (NIH, Bethesda, USA). Thrombus height was calculated by imaging the thrombi using the Apotome 2 confocal unit on the Zeiss Axio Observer (x63 oil immersion objective, 1.4 NA (Zeiss, Cambridge, UK)). Images were taken at 0.5 μm depth from the top of the thrombus to the bottom. All thrombi in a field of view were identified and the total height of the thrombi identified.
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Zeiss Microscope Imaging Protocol

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Images were acquired on: Zeiss AxioObserver inverted microscopes equipped with Axiocam HR or Axiocam 506 color cameras; a Zeiss AxioObserver inverted microscope equipped with CSU-X1 laser spinning disk (Yokogawa) and Orca Flash 4.0 camera (Hamamatsu Photonics); or a Zeiss LSM 880 scanning laser confocal microscope with Fast Airyscan and GaAsP detectors. Images were corrected for color balance and adjusted for display levels as necessary with conditions within analyses treated identically.
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Fluorescence Microscopy Imaging Protocol

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Slides were imaged with Axio Observer (Zeiss) microscope or with Zeiss LSM 510 Meta confocal mounted on an AxioObserver inverted microsope using the 63x oil objective. Images were taken with DAPI and GFP channels.
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Bright-field and Fluorescence Microscopy

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Bright-field and fluorescence images of the microwells and PDMS devices were taken using an inverted microscope (Axio Observer, Zeiss, Germany) with 5 × objective lenses, and a digital SLR camera (D300s, Nikon). For fluorescence imaging the green filter (XF100-2 Omegafilters, USA) was used. The 3 mm microwell was imaged using Axiocam 506 mono (Zeiss) on an inverted microscope (Axio Observer, Zeiss). All images were processed with Zeiss ZEN lite (Zeiss).
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7

Neuron Imaging in Microfluidic Devices

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Videorecording of neurons plated in microfluidic devices was performed at DIV 12. Before recordings, DIV 12 neurons in the microchamber were carefully inspected and selected based on the absence of cell contamination. For double transductions (with sh-RNA lentiviruses), the transport of mCherry-tagged cargo was analyzed within GFP-positive axons. Images were acquired every 200 ms for 1 min on an inverted microscope (Axio Observer, Zeiss) with X63 oil-immersion objective (1.46NA) coupled to a spinning-disk confocal system (CSU-W1-T3; Yokogawa) connected to an electron-multiplying CCD (charge-coupled device) camera (ProEM+1024, Princeton Instrument) at 37°C and 5% CO2.
For the study of the exocytosis events, images were acquired every 200 ms for 1 min on an inverted microscope (Axio Observer, Zeiss) with X63 oil-immersion objective (1.46NA) coupled to a spinning-disk confocal system (CSU-W1-T3; Yokogawa) with TIRF microscopy (Nikon/Roper, Eclipse Ti) equipped with a camera Prime 95B sCMOS (Telelyne Photometrics) at 37°C and 5% CO2. The same three fields per microchambers were acquired before and after a 4AP-bicuculline (respectively 2.5 mM and 50 µM) stimulation of the presynaptic chamber, four times in total (one before and three after stimulation).
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8

Drosophila Follicle Imaging Protocols

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Microscope images of fixed Drosophila follicles were obtained using LAS AF SPE Core software on a Leica TCS SPE mounted on a Leica DM2500 using an ACS APO 20×/0.60 IMM CORR -/D (Leica Microsystems, Buffalo Grove, IL), Zen software on a Zeiss 880 mounted on Zeiss Axio Observer.Z1 using Plan-Apochromat 20×/0.8 working distance (WD) = 0.55 M27, Plan-Apochromat 40×/1.3 oil Differential Interference Contrast (DIC) WD = 2.0 or Plan-Apochromat 63×/1.4 oil DIC f/ELYRA objectives, or Zen software on a Zeiss 700 LSM mounted on an Axio Observer.Z1 using a LD C-APO 40×/1.1 W/0 objective (Carl Zeiss Microscopy, Thornwood, NY). Maximum projections (two to five confocal slices), merged images, rotation, cropping, and distance measurements were performed using ImageJ software (Abramoff et al., 2004 ).
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9

Biodistribution of Nanoparticles in Mice

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At 1, 3, 7, 14, 30, 60, and 90 days post-injection, the mice in each group were sacrificed. The organs (heart, liver, spleen, lung, kidney, brain, and testis) were harvested. Frozen sections were obtained using a freezing microtome (CM3050S, Leica, Germany). Fluorescent images of these organs were obtained using a fluorescence microscope (Axio Observer, Zeiss, Germany).
Following organ harvesting, the organs were fixed in 10% formalin for 24 h, and then dehydrated with different gradient concentrations of alcohol. Before staining with H&E, the tissues were embedded in paraffin and sectioned. After staining, the stained slices were observed under a fluorescence microscope (Axio Observer, Zeiss, Germany).
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10

Amyloid-β Peptide Labeling and Characterization

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All commercially-available reagents and solvents were used as received without further purification. FAM-NHS was purchased from Lumiprobe Corp (Hunt Valley, Maryland, USA), sealed with parafilm and stored at −20°C. The purity and stability of the dye were monitored every 6 months using liquid chromatography mass spectrometry (LC-MS). Human amyloid-β peptide (1–42) was obtained from Anaspec (Fremont, CA, Cat. AS-20276). Ultrapure water (18.2 MΩ) was obtained from a Millipore Direct Q-5 water purification system. A Hitachi HPLC system (Lachrom Elite) equipped with a diode array detector was used for purification, and employed a Cytiva HiTrap Desalting column with a mobile phase of 25 mM sodium phosphate, 150 mM sodium chloride, pH7.4. Three fluorescence microscopes were used in our studies, including a manual Zeiss Axio Observer, an automated Zeiss Axio Observer, and a Zeiss LSM 710 confocal laser scanning microscope. MALDI-TOF analysis was performed on a Bruker Rapiflex with sinapinic acid matrix.
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