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44 protocols using dfc320 digital camera

1

Embryonic in situ Hybridization

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E13.5 embryos were isolated in ice cold PBS and fixated overnight in 4% paraformaldehyde in PBS, dehydrated in a graded ethanol series, embedded in paraplast and sectioned at 10 µm. Non-radioactive in situ hybridization on sections was performed as previously described (Moorman et al., 2001 (link)) using mRNA probes for the detection of Tbx3, Tbx5 and Hcn4. Stained sections were examined with a Zeiss Axiophot microscope and photographed with a Leica DFC320 Digital Camera.
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2

Quantitative Analysis of Neurodegeneration

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For immunostained sections, digital images were captured with an Olympus BX50 microscope equipped with a Leica DFC 320 digital camera. To count TH-immunopositive cells, every fourth section of each mouse brain was stained. TH-immunopositive neurons were quantified stereologically on regular spaced sections. To measure DAT and alpha-synuclein expression the optical density in the area of interest was measured and corrected for non-specific background. Stereology was performed to quantify the number of CD3 positive cells in the colon on regular spaced sections. Analysis were performed by researchers that were blind to the treatment condition of the animal. Immunofluorescence images were made using a Keyence BZ-9000 microscope. The Corrected Total Fluorescence (CTF) was calculated with the formula: integrated density − (area × mean fluorescence of background reading).
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3

Whole-mount in situ Hybridization Protocol

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Whole-mount RNA in situ hybridization was carried out using probes made by in vitro transcription with T7 or SP6 RNA polymerase (Promega Corporation, Madison, WI, USA). Templates were generated by PCR using the following primers: 5′-GTCTAATCCTTGCCGTCACC-3′ (Forward, SP6), and 5′-TAAGAACTTCCGCCCAGATG-3′ (Reverse, T7), common to the v1 and v2 isoforms. PCR was performed on cDNA from 1 dpf wild-type embryos. The probe and template sequences were verified.
For histological analysis, stained embryos were fixed in 4% paraformaldehyde, dehydrated, wax embedded, sectioned (8 μm) with microtome (Leitz 1516) and stained with eosin. Images were taken with an Olympus BH2 microscope, equipped with a Leica DFC 320 digital camera and IM50 software (Leica).
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4

Quantifying Osteoclast Activity in Bone

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Osteoclast numbers were determined according to the American Society for Bone and Mineral Research (ASBMR) system31 in paraffin sections from decalcified tibias stained for tartrate resistant acid phosphatase (TRAP) activity, counterstained with Aniline blue, and imaged using a Leica DMLB2 microscope and DFC320 digital camera.28 For each sample, sections from two separate levels (n = 2 slides) were photographed at magnification ×100 and a 1‐mm × 1‐mm ROI commencing 250 µm below the growth plate was analyzed. Osteoclast numbers per bone perimeter (Oc.N/B.Pm), osteoclast perimeter (Oc.Pm), and osteoclast surface per bone perimeter (Oc.S/B.Pm) were determined in trabecular bone and normalized to total bone perimeter (B.Pm).31 The fraction of bone surfaces that displayed osteoclastic bone resorption was also quantified in high‐resolution BSE‐SEM images.28
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5

Seedling Hypocotyl Measurement Protocol

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At 6 d post‐germination (dpg), seedlings were sampled 1 h after the initiation of the light cycle and photographed with a Canon EDS 1300D digital camera. Fifteen seedlings were sampled of each genotype and experiments repeated at least twice (n > 30). Hypocotyl lengths were measured using NIH ImageJ software (Schindelin et al., 2012 (link)).
To determine hypocotyl cell number and length, 6 dpg seedlings sampled 1 h into the light cycle and mounted in water were photographed using a Zeiss Axiophot microscope (Auckland, New Zealand), Leica DFC320 digital camera (Hobsonville, New Zealand), and Leica image software. The lengths of each of the individual hypocotyl cells in a protruding epidermal cell file were measured using ImageJ software. Cell numbers and lengths were measured for eight hypocotyls of each genotype.
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6

Quantifying Osteoclasts in Decalcified Tibias

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Sections from decalcified tibias were stained for tartrate-resistant acid phosphatase and imaged using a Leica DM LB2 microscope and DFC320 digital camera (8 (link), 23 (link)). A montage of nine overlapping fields covering an area of 1 mm2 located 0.2 mm below the growth plate was constructed for each bone. BV/TV was measured, and osteoclast numbers and surface were determined in trabecular bone normalized to total bone surface (23 (link)).
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7

Lung Tissue Histological Analysis

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After mice were sacrificed on day 56, lungs were fixed with 10% formalin infusion through a tracheal cannula at a constant pressure of 25 cm H2O. The lungs were immersed in fixative for at least 24 h, after which the left lung was embedded in paraffin. After paraffin embedding, 5 μm sections were cut and de paraffin sections were first deparaffinised. Endogenous peroxidase activity was blocked with 0.3% H2O2 (Merck) in methanol for 30 min at room temperature and rehydrated in a graded ethanol series to PBS and paraffin section were stained with hematoxylin/eosin (H&E) for inflammation, periodic acid-schiff (PAS) for goblet cells, Masson’s trichrome for connective tissue, rabbit polyclonal anti-α-smooth muscle actin antibody (Abcam, Cambridge, UK) for smooth muscle cells and rabbit polyclonal anti-Ki76 antibody (Abcam) for proliferating cells according to standard methods. Photomicrographs were taken with an Olympus BX50 microscope equipped with a Leica DFC 320 digital Camera.
Slides were reviewed in blinded fashion by two observers independently and slides were scored on the basis of the percentage of positive stained cells in the following way: -, no positive staining; +/-, less than 25% of cells stained positive; +, 25 to 50% cells stained positive; ++, 50 to 75% cells stained positive.
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8

Lung Tissue Fixation and Sectioning

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After lung lavage, lungs were fixated with 10% formalin infusion through the cannula at a constant pressure of 25 cm H2O. After at least 24 h of fixation lungs were embedded in paraffin. After embedding, 5 μ sections were cut and stained with hematoxylin/eosin (H and E) according to standard methods. Photomicrographs were taken with an Olympus B × 50 microscope equipped with a Leica DFC 320 digital Camera (Akbari et al., 2014 (link); Sagar et al., 2014b (link)).
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9

Histological Analysis of Wound Tissue

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After euthanasia, wounds with surrounding tissues were excised and fixed with 10% phosphate-buffered (pH = 7.4) formalin. The samples were transversely cut exactly through the center of the wound, dehydrated, and paraffin-embedded according to the routine protocols. Cross sections (5 μm thick) were stained with hematoxylin and eosin (H&E) and Mallory's trichrome stain. For immunostaining, sections were treated with 3% H2O2 for 10 min and then with 10% nonimmune goat serum before incubation with rabbit polyclonal antibodies against α-smooth muscle actin (α-SMA) and CD31 (Abcam, UK) or rat monoclonal antibodies against f4/80 (Serotec, UK). Goat anti-rabbit and anti-rat IgG biotinylated antibodies (Vector, USA) were applied and stained with avidin-peroxidase conjugate and diaminobenzidine (Vector, USA). Before CD31 staining, heat-mediated antigen retrieval with Vector Antigen Unmasking Solution (Vector, USA) at 98°C for 40 min was applied additionally.
Samples were analyzed with a DM 5000B microscope equipped with a DFC 320 digital camera (Leica, Germany).
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10

Quantifying Osteoclast Parameters in Bone

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Osteoclast numbers were determined according to the American Society for Bone and Mineral Research system (35 (link)) in paraffin sections stained for TRAP activity using a Sigma TRAP kit (386A-1KT) according to manufacturer's instructions. For each sample sections from 2 separate levels (n = 2 slides) were photographed at ×100 magnification using a Leica DMLB2 microscope and DFC320 digital camera, and a 750 × 750-μm ROI commencing 250 μm below the growth plate was analyzed. Osteoclast numbers per bone perimeter (Oc.N/B.Pm), osteoclast perimeter (Oc.Pm), and osteoclast surface per bone perimeter (Oc.S/B.Pm) were determined in trabecular bone (n = 3–5 mice per genotype, per gender) and normalized to total bone perimeter (B.Pm) (30 (link)). The fraction of the bone surfaces that displayed osteoclastic bone resorption was quantified in high-resolution BSE-SEM images (30 (link)).
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