Movies were analyzed by using the Region Measurements function of Metamorph software (Universal Imaging, Downingtown, Pa). Threedimensional (3D) projection of degranulated mast cells was obtained by using the interactive 3D surface plot (Image J), and 3D reconstruction of degranulated mast cell in Matrigel was obtained with Imaris software (Bitplane; Oxford Instruments, Abingdon, United Kingdom). Colocalization analysis was performed with the Linescan function of Metamorph software (Universal Imaging).
Metamorph software
Manufactured by Universal Imaging
Sourced in United States, Japan, Germany, United Kingdom, Cameroon, France, Azerbaijan, Canada
MetaMorph is an imaging software that enables the acquisition, processing, analysis, and visualization of digital images. It provides a comprehensive suite of tools for researchers and scientists to examine and quantify various biological and microscopic samples.
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Lab products found in correlation
Coolsnap hq ccd camera, by Teledyne (8 mentions)
Sutter filter wheel, by Teledyne (7 mentions)
Eclipse ti, by Nikon (6 mentions)
Axio observer z1, by Zeiss (6 mentions)
Dmire2 microscope, by Leica (5 mentions)
Sp5 confocal microscope, by Leica (5 mentions)
Coolsnap hq2 ccd camera, by Teledyne (5 mentions)
Eclipse ti, by Teledyne (4 mentions)
Ix83 microscope, by Olympus (4 mentions)
Eclipse ti e inverted microscope, by Nikon (4 mentions)
Ix81 microscope, by Olympus (4 mentions)
Anti rabbit cy3, by Merck Group (4 mentions)
Coolsnap hq, by Teledyne (3 mentions)
Evolve emccd camera, by Teledyne (3 mentions)
Orca er camera, by Hamamatsu Photonics (3 mentions)
Axiovert 200m microscope, by Zeiss (3 mentions)
Csu x1 m1, by Yokogawa (3 mentions)
Cooled charge coupled device camera, by Teledyne (3 mentions)
4 6 diamidino 2 phenylindole (dapi), by Merck Group (3 mentions)
Anti mouse oregon green, by Thermo Fisher Scientific (3 mentions)
278 protocols using metamorph software
1
Analyzing Mast Cell Degranulation in 3D
2
Fluorescence Microscopy Techniques for Actin
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Most of the experiments were done with an epifluorescence system (Ti2 Nikon inverted microscope equipped with a Hamamatsu Orca Flash 4.0 LT Plus Camera). The following objectives were used: Plan Fluor 10X DIC and S Plan Fluor ELWD 20X DIC. Time lapse were acquired with the NIS elements software (version 4.60).
Z‐stacks of microwells were performed with a confocal spinning disk system (EclipseTi‐E Nikon inverted microscope equipped with a CSUX1‐A1 Yokogawa confocal head), an Evolve EMCCD camera (Photometrics), Plan Fluor 60X objective. Z‐stacks were acquired with Metamorph software (Universal Imaging).
FRAP, k + estimation and visualization of branched actin network formation was done on a total internal reflection fluorescence (TIRF) microscopy instrument composed of a Nikon Eclipse Ti, an azimuthal iLas2 TIRF illuminator (Roper Scientific), a × 60 NA1.49 TIRF objective lens and an Evolve EMCCD camera (Photometrics). Time lapse and FRAP were done with Metamorph software (Universal Imaging).
Z‐stacks of microwells were performed with a confocal spinning disk system (EclipseTi‐E Nikon inverted microscope equipped with a CSUX1‐A1 Yokogawa confocal head), an Evolve EMCCD camera (Photometrics), Plan Fluor 60X objective. Z‐stacks were acquired with Metamorph software (Universal Imaging).
FRAP, k + estimation and visualization of branched actin network formation was done on a total internal reflection fluorescence (TIRF) microscopy instrument composed of a Nikon Eclipse Ti, an azimuthal iLas2 TIRF illuminator (Roper Scientific), a × 60 NA1.49 TIRF objective lens and an Evolve EMCCD camera (Photometrics). Time lapse and FRAP were done with Metamorph software (Universal Imaging).
3
Quantifying Spindle Pole Tubulin Dynamics
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Images were acquired using a Plan‐APO 60×/1.4NA objective on a Ti Nikon microscope enclosed in a thermostatic chamber (Life Imaging Service) equipped with a Flash4.0 V2 CMOS camera (Hamamatsu) coupled to a Yokogawa CSU‐X1 spinning disk. Metamorph Software (Universal Imaging) was used to collect data. All oocytes expressed SiR‐Tubulin (from Spirochrome reference SC002, used at 0.1 μM). For all oocytes, an identical region of interest (diameter of 5 μm) was bleached at spindle poles. Images were acquired every 5 s for 125 s. One image was taken before bleaching. The SiR‐Tubulin fluorescence intensity quantification was performed using the Metamorph Software (Universal Imaging). Normalization of the measured fluorescence intensities was performed using the Microsoft Excel software. As the expression levels of SiR‐Tubulin vary from one experiment to another, the signal intensity was normalized so that the prebleached value was 1 and the value at the first time point after bleaching was 0.
4
Live-cell Fluorescent Imaging Microscopy
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A Leica DMRXA2 microscope with 100× objective and a Hamamatsu digital camera interfaced with METAMORPH software (Universal Imaging) was used. Cell morphology and localization of fluorescent protein were visualized in living cells without fixing. Nuclei were stained using mounting medium with DAPI (Vectashield®). Time-lapse microscopy was performed on an inverted confocal laser LSM700 microscope (Carl Zeiss) with an attached temperature chamber and a photometrics coolsnap HQ2 digital camera interfaced with METAMORPH software (Universal Imaging). 1× GMM with 2% agarose or 1× MalMM with 2% agarose was spotted onto glass slides and cooled. Live cells were mounted onto the agar and covered with a cover slip and sealed. Image recoloring and sum projection of z-stacks was performed using Fiji (http://fiji.sc/Fiji ).
5
Immunocytochemistry Visualization of HIF1α
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For the immunocytochemistry, UCB-MSCs were fixed with 4% paraformaldehyde (PFA; Lugen Sci, Seoul, Korea, #LGB-1175) for 10 min, and then incubated in 0.5% Tween-20 for 10 min. Cells were incubated with primary antibodies in PBS containing 0.1% Tween-20 (PBST; 1:100 dilution) for 2 h and washed with PBS three times. Cells were incubated with Alexa Fluor™ 488 or 555-conjugated secondary antibodies in PBST (1:100 dilution) for 1 h. Immunofluorescence stained samples were visualized by a super-resolution radial fluctuations (SRRF) imaging system (Andor Technology, Belfast, UK) [35 (link)]. Relative fluorescence intensities of HIF1α, HIF1α/BICD1 and HIF1α/Dynein IC were quantified with the ImageJ software. The co-localization rate of HIF1α with BICD1 was analyzed with the MetaMorph™ software (Universal Imaging, West Chester, PA, USA).
6
Arterial Thrombus Formation Assay
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Thrombus formation was evaluated by perfusing whole blood over collagen-coated micro-channels under arterial shear conditions. Briefly, Vena8 FLUORO+ Biochips (Cellix Ltd) were coated overnight at 4°C with fibrillar collagen (50 μg/ml) and blocked with Hank’s Balancing Salt Solution containing 0.1% BSA. Whole blood from the various mice to be tested was anti-coagulated with heparin and PPACK, labeled with mepacrine (CalBiochem), and perfused over collagen-coated micro-channels at a shear rate of 1333s-1. Images of platelet adhesion and thrombus formation were acquired by epifluorescence microscopy in real time at a frame rate of one frame per second. Quantification of thrombus formation is reported as the mean integrated fluorescence intensity (IFI) per μm2. Image analysis was performed using Metamorph software (Universal Imaging).
7
Cell Morphology and DNA Repair Protein Localization
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Images and cell length measurements were obtained using an Olympus IX71 microscope equipped with a personal Delta Vision system and a Photometrics CoolSnap HQ2 monochrome camera, with Metamorph software (Universal Imaging, Molecular Devices, Downingtown, PA, USA). Measurements were made from micrographs using the IMAGEJ (National Institutes of Health). All microscopy was conducted on live midlog-phase cells placed on slides, except for cultures for DAPI and aniline blue staining, which were fixed in 70% ethanol at room temperature, washed, and pelleted before resuspension in 5 μl of DAPI solution (500 μg/ml). More than 200 dividing cells per strain were measured for the cell length data. Stacks of ten z-series sections were acquired at 0.2-μm intervals. All fluorescence images are maximum two-dimensional (2D) projections of z-series and were analyzed using deconvolution software from Applied Precision. To calculate the area of the nucleus occupied by Rad52p-YFP a binary mask was created using the mean value of the nuclear background without foci as a threshold and measuring the area of this mask. To detect Rad51p indirect immunofluorescence microscopy was performed according to the protocol described in (46 (link)). The rabbit polyclonal anti-human Rad51p (PA5-27195, Thermo Fisher, Rockford, IL, USA) was diluted 1.100.
8
Localization of Stress Response Proteins
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Localization of Ssk1-GFP and Hog1-GFP were performed as described [8 (link)]. Overnight cultures of cells expressing Ssk1-GFP and Hog1-GFP were diluted in the morning to an OD600 ~ 0.1 in HC-Leu with 1μg/mL of DAPI and grown for three doubling times to early log phase (OD600 ~ 0.8–1.0). Aliquots of cell were left in HC-Leu or washed once in HC-Leu without 2% glucose (HC-Leu-Glc) and incubated for 30 min in HC-Leu-Glc or submitted to osmotic stress with 0.4 M NaCl (HC+NaCl) for 5 min. GFP and DAPI signals in living yeast cells were viewed using a Nikon fluorescence microscope (model E800) equipped with a Plan-Apo 100x/1.4 oil objective and a Photometrics Coolsnap HQ camera. Images were analyzed using Metamorph software (Universal Imaging Corporation).
9
Visualizing Surface GluN Receptors
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Neurons co-transfected with Homer1c-DsRed and either GluN2A-SEP or GluN2B-SEP were placed on the heated stage (37 °C) of an inverted confocal spinning-disk microscope (Leica). To test the population of surface GluN subunits-SEP, we used low pH-solution adjusted to pH 5.4 which quenched all the fluorescence indicating that SEP allows the specific visualization of surface receptors33 (link). Fluorescence was excited using a monochromator and cluster fluorescence intensity was followed over time to assess synaptic receptor content. Clusters were imaged over a total period of 35 minutes (corticosterone was applied after a 5 min baseline; the medium was carefully replaced by new equilibrated and heated medium after the protocol application). Fluorescence intensity was measured using Metamorph software (Universal imaging, USA) and corrected for photobleaching and background noise.
10
Quantifying Cell Proliferation in Lung Tissue
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Proliferation was quantified in lung tissue from five random noncontiguous fields of lung parenchymal/distal air space saccules from at least four separate animals in each group. Fields that contained a large airway or blood vessel were not used for the analysis. Each field was photographed at 40-fold magnification using a Zeiss Axiophot microscope (Zeiss, Oberkochen, Germany) and AGFA RSX II FILM (Agfa-Gevaert, Leverkusen, Germany; ASA 50). Quantification was performed using Metamorph software (Universal Imaging, Downingtown, PA). Metamorph was configured to measure the total number of nuclei based on the average area of a nucleus. The total number of cells that stained positive for Ki67 were counted manually using Metamorph to mark the counted cells. The total number of nuclei and the number of positively stained nuclei in each field were determined; 400–600 nuclei per field were counted for each tissue section. The frequency of Ki67+ cells was calculated as a percentage of the total cell nuclei in the alveolar (cells lining the distal air sacs and alveoli) and bronchiolar epithelial cells for each treatment group (n = 4–5 mice/group).
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