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31 protocols using ck40 inverted microscope

1

Breast Cancer Cell Colony Formation

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For the colony formation assays, BT474 TRZ_R and HCC1954 breast cancer cells were plated into 6-well plates (2 × 103 cells/well) and incubated at 37 °C, O/N. The next day, the cells were treated with 2 μM ponatinib or sunitinib (Selleck Chemicals) and then incubated for an additional 10 days. Cell colonies were fixed with 10% ethanol, stained with 0.01% crystal violet, and observed using a CK40 inverted microscope (Olympus, Tokyo, Japan).
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2

Evaluating Embryoid Body Growth Dynamics

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To evaluate EB growth dynamics and patterning, the EBs (24 EBs/per stage; three experiments; N = 288 for each cell line) cultivated in 12 or 96-well plates with a low-attachment surface (Greiner Bio-One International GmbH and Nunclon Sphera; Nuclon) and imaged at the studied stages. The EB images were captured using Olympus CK40 inverted microscope equipped with a Camedia C-4040 camera (Olympus). EB diameters were measured in 2-8 directions for average calculation using ImageJ/Fiji software (https://imagej.nih.gov/ij/) with prior set up absolute scale calibration (see Supplementary Methods). EB volumes, volumetric pattern sizes and their ratios were calculated using Excel.
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3

Follicle Morphology Assessment Protocol

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Follicle survival, growth and antrum formation were assessed weekly using an Olympus CK-40 inverted microscope and an Olympus DP11 digital camera (Olympus Imaging America Inc., Center Valley, PA, USA), as described previously22 (link). Follicle growth was determined by measuring the distance from the outer layer of cells at the widest diameter and then the diameter perpendicular to the first measurement by the same individual. The mean of the two values determined the follicle’s overall diameter. The measurements were performed using ImageJ 1.6.0 software (National Institutes of Health, Bethesda, MD, USA). Follicles were considered atretic if the oocyte was dark or not surrounded by a layer of granulosa cells, the granulosa cells appeared dark or fragmented, or the follicle diameter decreased.
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4

Wound Healing Assay with TNBC Cells

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MDA231, Hs578T, and HCC1806 TNBC cells were seeded in 6-well plates and cultured for 24 h. Then, the TNBC cells were maintained in culture medium without FBS for 16-24 h. The cell monolayer was scratched with a 200-μL pipette tip to create a wound, which was washed twice with PBS to remove the suspended cells. TNBC cells were maintained with or without 10 μM LY2109761 for 24 h in serum-containing medium. The cells migrating from the leading edge were photographed at 0 and 24 h using a CK40 inverted microscope (Olympus, Tokyo, Japan). Cell to cell distance was analyzed average of pixel number on three sites using Axiovision software (Carlzeiss, Thornwood, NY).
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5

Breast Cancer Cell Colony Formation Assay

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MCF-7 and T47D breast cancer cells were plated onto 6-well tissue culture plates (2×103 cells/well) for the colony formation assay. After 24 h, the cells were treated with 2 µM specific inhibitors (ponatinib and sunitinib; Selleck Chemicals), followed by an additional incubation for 10 days. Subsequently, the colonies were fixed in 10% ethanol for 5 min at RT and stained with 0.01% crystal violet for 30 min at RT and observed using a CK40 inverted microscope (magnification, ×20; Olympus Corporation).
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6

Myotube Morphology Assessment

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The morphologies of myotubes were observed using a CK40 inverted microscope (Olympus, Japan) equipped with a T500 camera (magnification, ×200; eXcope, Korea). The random areas of each group were captured and the diameters were measured using the Image J software (National Institutes of Health, USA).
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7

Microscopic Analysis of Cellular Morphology

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Morphological features were studied under an Olympus CK40 inverted microscope at 20× magnification. Images were captured using VisiCam software (VWR, USA).
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8

Microscopic Morphological Analysis

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Morphological features were studied under an Olympus CK40 inverted microscope at 40 x magnification. Images were captured using VisiCam® software (VWR, USA).
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9

Quantifying Hepatic Lipid Deposition

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After liver samples were collected, one fresh section of liver tissue from each rat was used to prepare frozen sections. Each section was incubated in liquid nitrogen for 4–10 s prior to staining with Oil Red O (Sigma-Aldrich, St. Louis, MO, USA). The mean optical density (MOD) was calculated to quantify the intracellular lipid deposition, using the image analysis software Image Pro-plus 6.0 (Media Cybernetics, USA). One more fresh section of liver tissue from each rat was fixed by immersion in 10% buffered formalin for paraffin wax embedding prior to staining with H&E. The histological examination was performed by a pathologist blinded to the rats' data. The samples were observed using an Olympus CK40 inverted microscope (Olympus, Tokyo, Japan).
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10

Zooplankton and Microplankton Abundance Quantification

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A minimum of 200 non-naupliar organisms were subsampled from aliquots of each zooplankton sample using a Stempel pipette, which were examined using a Leica MZ6 stereomicroscope (Leica Microsystems) at 40X magnification. Specimens were identified to the lowest possible taxonomic rank using Thorp and Covich [35 ], with most rotifers and microcrustaceans identified to the genus or species level. We converted counts of individual taxa to density (individuals m–3) by multiplying each count by the ratio of sample volume to subsample volume, and then dividing by the total volume of water filtered. Two replicate samples were processed for each sampling date.
Microplankton samples (i.e. planktonic protists, eukaryotic algae, cyanobacteria) were taxonomically processed via 1–10 ml subsamples of the Lugol’s preserved water samples. Subsamples were settled overnight in Utermohl chambers, and the chambers examined using an Olympus CK-40 inverted microscope at 200X (numerical aperture = 0.75). All individuals were identified to genus (and species when possible) using Wehr et al. [58 ] and sized using an ocular micrometer in order to calculate biovolume and carbon biomass based on geometric shape [59 (link), 60 (link)].
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