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64 protocols using axiocam hrc digital camera

1

Collagen Fiber Analysis in Cornea

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After transmittance measurements, the corneas were fixed with 4% buffered paraformaldehyde and embedded in paraffin. Sections 5-μm thick were stained with Picrosirius-red (0.1% Sirius red in saturated aqueous picric acid for 1 h) (Junqueira et al., 1979) . Sections were examined under an Axiophot microscope (Zeiss Axiophot HBO-50; Carl Zeiss, Oberkochen, Germany) with polarized light. Photomicrographs were captured using the AxioCam HRc Digital Camera and Axiovision release 4.8 software (Carl Zeiss) under the same plane of polarization. Polarization colors are associated with different collagen fiber thicknesses, packing density, and spatial arrangement (Dayan et al., 1989) . Orange to red colors were correlated with thick collagen fibers that were tightly packed and well aligned. Yellowish-green colors were correlated with thinner fibers that were less tightly packed.
Other 5-μm sections were stained with a modification of the Gomori's Silver Impregnation technique to demonstrate the presence of collagen type III fibers [54] . The sections were examined under an Axiophot microscope (Zeiss Axiophot HBO-50; Carl Zeiss, Oberkochen, Germany) and photomicrographs were obtained with an AxioCam HRc Digital Camera and Axiovision release 4.8 software (Carl Zeiss).
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2

Colonic Crypt Morphometry and Goblet Cell Analysis

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Serial sections of the colon, with a thickness of 5 µm, were collected and subsequently deparaffinized in xylene, rehydrated with different alcohol solutions, and stained with hematoxylin and eosin.
Histological sections were visualized in an Olympus AX70 photomicroscope, and the images were captured in a 20X objective with an AxioCam HRc—Zeiss digital camera. The following features were analyzed: crypt depth, crypt width, and the number of goblet cells. For that, we randomly selected six animals per group and twenty random fields per animal, analyzing one crypt per field. Only crypts with a well-defined and visible structure were used.
The measurements of the crypts were performed using the ImagePro-Plus® version 4.5 software (Media Cybernetics Inc., 1700 Rockville Pike, Suite 240, Rockville, MD 20852, USA) and the goblet cell count was performed using the Image J® 1.48v software (Research Services Branch, National Institute of Mental Health, Bethesda, MD, USA).
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3

Histopathological Analysis of Anorectal Tissue

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On day 60 (D60), the rats were euthanized by intracardiac administration of 150 mg/kg sodium thiopental, after proper anesthesia. The samples from the anorectal region were collected surgically in a uniform way and volume. Samples were weighed on analytical balance, fixed in 10% formaldehyde, processed to histological study and stained in hematoxylin-eosin and Masson trichrome.
The histopathological analysis was done at 400x using an Axio Imager.M2m/Zeiss microscope coupled to an AxioCam HRc/Zeiss digital camera. The volumetric density of blood vessels as well as cell populations were evaluated using a M42 system [grade] test, projected by ImageJ Software. The pictures were taken and transferred to a computer and analyzed using ZEN 2012 Software/Zeiss.
The collagen presence was analyzed by systematically assessing the newly-formed collagen in a semiquantitative manner. Then, the slides were classified as G0, GI, GII or GIII, based on the percentage of recently formed collagen as compared to total. That percentage was calculated based on classic quantitative morphometry [20 (link), 21 ].
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4

Histological Tissue Analysis with IHC

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Tissues were fixed in either 4% formalin or acidified formaldehyde (ethanol/acetic acid/formaldehyde/saline at 40:5:10:45 v/v). Sections were prepared at 2 µm thickness from the paraffin blocks and stained with haematoxylin and eosin (HE) according to standard procedures. For immunohistochemistry (IHC), 4 um-thick sections were made. Antibodies used in this study are listed in Supplementary Table 4.
Antibody staining was revealed using either diaminobenzidine or 3-amino-9-ethylcarbazole chromogen. Images were captured using a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy) equipped with a Zeiss AxioCam HRc digital camera, and processed using AxioVision 4 software (Carl Zeiss Vision).
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5

Quantitative Analysis of Vimentin in Tumor Tissue

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Lung and liver tissues were collected and fixed in formalin fixative and embedded in paraffin. The immunohistochemistry (IHC) of vimentin (DAKO, M0725, dilution: 1:4,000) was conducted on 4‐μm‐thick sections according to standard procedures. The stained slides were examined blindly by a pathologist, and the number of tumorous lesions (more than 10 cancer cells) was scored in each of the sections. The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy, Jena, Germany), and images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision, München, Germany).
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6

Paraffin-Embedded Tissue Histology

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Tissues and organs were collected and fixed in EAF fixative (ethanol:acetic acid:formaldehyde:saline at 40:5:10:45 v:v) and embedded in paraffin. Sections were prepared at 2 µm thickness from the paraffin blocks and stained with haematoxylin and eosin according to standard procedures. The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy) and images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision).
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7

In Situ Hybridization of Nematostella Transcripts

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In situ hybridization of transcripts for cloned genes was performed using protocols established for chromogenic detection in the cnidarian Nematostella vectensis [56 (link)]. A detailed protocol is presented in Additional file 3. Hybridization was performed at 62°C for 48 h with DIG-UTP-labeled probes at a concentration of 1 ng/μL. Detection of hybridized probes was performed by staining with NBT and BCIP, after labeling with alkaline phosphatase-conjugated anti-DIG antibody. At least 20 embryos were processed per stage for each gene, and development of staining was checked by a stereomicroscope prior to completion of the in situ protocol and mounting for imaging. In all cases, staining was highly consistent within stages. Embryos were cleared and mounted in 80% glycerol, and imaging was performed on a Zeiss AxioSkop microscope equipped with Plan-Apochromat 20×/08 N.A. objective and differential interference contrast optics (Carl Zeiss, Jena, Germany). Images were acquired with a Zeiss AxioCam HRc digital camera and Zeiss AxioVision v4.8 software (Carl Zeiss, Jena, Germany).
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8

Histological and Immunohistochemical Analysis of Lung Tissues

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For histological analysis, lungs were inflated and fixed for 24 h with ethanol–acetic acid–formalin (EAF). Fixed tissues were subsequently dehydrated, embedded in paraffin and sections of 2-4 μm were prepared, and stained with hematoxylin and eosin (H&E) for subsequent histopathological analyses. For IHC, tissue sections were rehydrated, blocked in BSA containing PBS, and sequentially incubated with specific primary antibodies and with biotinylated secondary antibodies (DAKO).
The following primary antibodies were applied: CGRP (Sigma, C8198),
E-cadherin/CDH1 (Cell signaling, 3195), FGFR1 (Cell signaling, 9740), GFP (Abcam, ab6556), ALDH1A1 (Abcam, ab23375), EGFR (Abcam, ab52894), SOX2 (Millipore, AB5603), SOX9 (Millipore AB5535), TTF1 (Agilent M357501-2), Synaptophysin/SYP (Abcam, ab32127).
The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy, Jena, Germany) and images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision, München, Germany).
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9

Docetaxel-Induced Histological Changes

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Three days after oral or intraperitoneal administration of docetaxel to mice, total body necropsy was performed and tissues and organs were fixed in EAF fixative (ethanol/acetic acid/formaldehyde/saline at 40:5:10:45 v/v) and embedded in paraffin. Sections were cut at 2 µm from the paraffin blocks and stained with hematoxylin and eosin (HE) according to standard procedures. The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy) equipped with Plan‐Apochroma and Plan‐Neofluar objectives. The reviewing animal pathologist was blinded to the dose level, route of administration and strain. Images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision, Munich, Germany).
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10

Histological Analysis of Organs

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Animals were sacrificed when they acquired respiratory distress. Tissues and organs were collected and fixed in EAF fixative (ethanol/acetic acid/formaldehyde/saline at 40:5:10:45 v/v) and embedded in paraffin. Sections were prepared at 2 μm thickness from the paraffin blocks and stained with hematoxylin and eosin (HE) according to standard procedures. For immunohistochemistry (IHC), 4 μm-thick sections were made on which the following antibodies were applied: Synaptophysin/SYP (Abcam, ab32127), E-cadherin/CDH1 (Cell Signaling Technology, 3195), NFIB (Thermo Fisher Scientific, PA5-28299), CGRP (Sigma-Aldrich, C8198), Ki67 (Abcam, ab15580), keratin wide-spectrum/KWS (Agilent, Z0622), phospho-histone H3/p-HH3 (Millipore, 04-746), Podoplanin/PDPN (Abcam, ab11936), ASCL1 (BD Biosciences, 556604), ALDH1A1 (Abcam, ab23375), NEUROD1 (Proteintech, 12081-1-ap), phospho-AKT (Cell Signaling Technology, 4060) and phospho-4EBP1 (Cell Signaling Technology, 2855). The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy) and images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision).
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