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16 protocols using aperio versa slide scanner

1

Whole-Brain Mapping of Hippocampal Inputs

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Whole-brain images were acquired of every section at 10X magnification with an Aperio Versa Slide Scanner (Leica Biosystems). Individual sections on each slide were isolated then registered to the Allen Brain Atlas using NeuroInfo software with Brainmaker module (MBF Bioscience) and all RV+ neurons outside of the hippocampus (with the exception of contralateral CA3)were mapped and counted. In ventral hippocampal sections, cells co-expressing mCherry and EGFP (starter cells) were imaged with a CSU-W1 spinning disk widefield confocal microscope (Nikon Imaging Center, UCSF) at 40X magnification, then registered to the Allen Brain Atlas using NeuroInfo (MBF Bioscience) and counted.
For each brain, the number of input neurons in a specific brain region was normalized to the total number of input neurons (RV+) counted across the brain outside of the hippocampus. All data collection and counts were made blinded to the experimental group. The mean and standard error of the mean are listed in Supplementary Data Table 3 for each brain region. For analysis one- way ANOVAs were run and those regions with P<0.05 were run with multiple t-tests with Holm-Sidak correction for multiple comparisons. All statistical results for significant effects are in Supplementary Data Table 4. Data was analyzed using Prism 8 (GraphPad).
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2

Whole-Brain Mapping of Hippocampal Inputs

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Whole-brain images were acquired of every section at 10X magnification with an Aperio Versa Slide Scanner (Leica Biosystems). Individual sections on each slide were isolated then registered to the Allen Brain Atlas using NeuroInfo software with Brainmaker module (MBF Bioscience) and all RV+ neurons outside of the hippocampus (with the exception of contralateral CA3)were mapped and counted. In ventral hippocampal sections, cells co-expressing mCherry and EGFP (starter cells) were imaged with a CSU-W1 spinning disk widefield confocal microscope (Nikon Imaging Center, UCSF) at 40X magnification, then registered to the Allen Brain Atlas using NeuroInfo (MBF Bioscience) and counted.
For each brain, the number of input neurons in a specific brain region was normalized to the total number of input neurons (RV+) counted across the brain outside of the hippocampus. All data collection and counts were made blinded to the experimental group. The mean and standard error of the mean are listed in Supplementary Data Table 3 for each brain region. For analysis one- way ANOVAs were run and those regions with P<0.05 were run with multiple t-tests with Holm-Sidak correction for multiple comparisons. All statistical results for significant effects are in Supplementary Data Table 4. Data was analyzed using Prism 8 (GraphPad).
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3

Histological Analysis of Batten Disease

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Brains were histologically examined for classic Batten disease pathology in the somatosensory cortex as this is one of the more commonly examined cortical regions that displays Batten disease pathology21 (link),22 (link). Female animals were sacrificed with pentobarbital at 17 months of age, and one hemisphere of the brain was placed into 10% neutral buffered formalin for approximately 3 weeks. The brain was sub-dissected into somatosensory cortex blocks and equilibrated in cryoprotectant solution (30% sucrose in TBSA) at 4 °C. Blocks were serial sectioned (50 µm) on a freezing microtome (Leica) and free-floating sections were used for standard immunohistochemistry13 ,23 (link)–27 (link). The following primary antibodies were used: anti-mitochondrial ATP synthase subunit C (Abcam, ab181243; 1:2000). Immunolabeled sections were scanned using an Aperio Versa slide scanner (Leica Biosystems, IL, USA) and at least 3 images were extracted from each region of interest and processed as previously published for total percent area of mitochondrial ATP synthase subunit c (SubC)13 ,23 (link),24 (link).
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4

Multimodal Imaging of Optogenetic Targets

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Images were obtained with a Zeiss LSM710 (Zen Blue Edition software, Zeiss) using the 405, 488, 561, and 594 laser lines, with appropriate emission filters to prevent optical bleed through. Sections containing the MeApd in both experiments were imaged with a 20× objective (Plan-APOCHROMAT 20×/0.8) for both 2D images, to confirm eNpHR or channelrhodopsin expression, and 3D images. In the Z-plane, the entire depth of the tissue was imaged. For experiment 2, the posteroventral region of the MeA (MeApv) was imaged as described as well. Sections containing the ARH and VMHvl were also imaged at 20×, in 2D only. Sections containing the MPN were imaged using a Leica Aperio VERSA Slide Scanner equipped with LAS X Life Science software suite (Leica Biosystems), using a 20× objective (HC PL APO 20×/0.8), resulting in a final optical magnification of 200×.
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5

ACE2 Expression in Canine Cardiac and Renal Tissues

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Cohorts of dogs that died or were euthanized for cardiac diseases and dogs that died from noncardiac reasons at the University of Pennsylvania were recruited. Sections of left kidney that included both cortical and medullary tissue and full thickness LV myocardial samples from the lateral wall of the ventricle just apical to the mid‐point of the paraconal coronary artery were obtained within 60 minutes of death. Kidney and myocardial samples were fixed in 10% neutral buffered formalin for up to 72 hours followed by sectioning. A rabbit polyclonal primary antibody against ACE2 (ARP53751‐P050, Aviva Systems Biology, San Diego, California) was used at a dilution of 1:1200 and incubated on the sections for 45 minutes at room temperature (RT). A biotin‐free polymeric IHC detection system consisting of horseradish peroxidase conjugated anti‐rabbit IgG then was applied for 25 minutes at RT. Finally, slides were counterstained in hematoxylin, scanned (Leica Aperio Versa slide scanner, Leica Biosystems, Buffalo Grove, Illinois), and images acquired (ImageScope, Leica Biosystems, Buffalo Grove, Illinois). Additional details regarding IHC methods can be found in the Supporting Information.
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6

Histopathological Evaluation of Pancreatic Neoplasia

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Formalin Fixed Paraffin Embedded (FFPE) mouse pancreatic tissues were H&E stained and histologically examined by board-certified veterinary pathologists (E.R. & C.-A.A.). Blind histopathological evaluation and classification of mouse pancreatic intraepithelial neoplasias (Pan-IN) in KC and KCC mice were performed according to established consensus criteria as previously described (20 (link)). The number of Pan-IN low grade (1 (link)–2 (link)) and high grade (3 (link)) lesions were counted. Slides were scanned at 20X magnification using a Leica Aperio Versa slide scanner (Leica Biosystems, Inc., Buffalo Grove, IL) and quantification of tissue area for each pancreas was performed using the Genie algorithm on the Aperio ImageScope software (Leica Biosystems, Inc., Buffalo Grove, IL). The percentage of each type of Pan-IN lesion was calculated using the formula: (#specific grade of Pan-IN/total # of Pan-INs) × 100.
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7

Visualization of Cardiac Hydrogel Distribution

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The chemically tagged rHC matrices (25 nmol of dye per hydrogel) were injected to the infarcted mouse heart, as described above. Animals were killed at 2 h, 2 days, and 7 days after treatment, and hearts were harvested and imaged ex vivo by IVIS® Spectrum (PerkinElmer) to visualize rHCI and rHCIII distribution within the hearts (λexcitation: 570 nm; λemission: 640 nm). For histology, tissue sections were prepared in acetone and then stained with DAPI followed by imaging using a Leica Aperio Versa slide scanner with a final magnification of ×20  and a Z-stack with eight steps at 1.5 μm.
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8

Immunohistochemistry Staining and Analysis

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Fixation and preparation of tissues were performed according to the published protocol.14 (link) For immunohistochemistry (IHC), tissue samples were cut into 3 µm thick sections from formalin-fixed paraffin-embedded tissues. IHC staining was performed using a Bond Max automated staining system (Leica) with the antibodies anti-PSMB8 (D1K7X, Cell Signaling, Cat. no. 13635) and anti-Calbidin D28k (CB300, Swant Inc., Cat. no. 300). Images were acquired using the Leica Aperio Versa slide scanner and Leica Aperio eSlide Manager software v. 1.0.3.37. IHC images were analysed quantitatively using the Aperio ImageScope software v. 12.3.2.8013.
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9

Quantifying IL-33+ Cells in Metastases

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Human patient samples were collected with written informed consent and processed at the Sheba Medical Center, Israel, in accordance with recognized ethical guidelines, under an approved Institutional Review Board (IRB) (3112-16). Tissue sections stained for IL-33 (AF3625, R&D systems) were analyzed by an expert pathologist. Images were scanned at X20 magnification using the Leica Aperio VERSA slide scanner. Analysis was performed using ImageScope software. In each slide, 5-10 areas of metastases and 5-10 normal areas were arbitrarily selected, and quantified for IL-33+ cells.
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10

Automated MYC Immunostaining Analysis

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Human patient samples were collected and processed at the Sheba Medical Center, Israel, under an approved Institutional Review Board (IRB) (3112-16). Sections stained for MYC were analyzed by an expert pathologist (Prof. Iris Barshack). Images were scanned at ×20 magnification using the Leica Aperio VERSA slide scanner. Analysis of the staining was performed using ImageScope software.
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