The largest database of trusted experimental protocols

28 protocols using scn400 scanner

1

Detecting Trpc1 Gene Expression in Mice

Check if the same lab product or an alternative is used in the 5 most similar protocols
Homozygous mice (Trpc1lacZ) were anesthetized and transcardially perfused with 4% paraformaldehyde in PBS. Brains were isolated, cryoprotected, and frozen sectioned (16 μm) in sagittal plane. For β-galactosidase activity detection, sections were fixed in 2% glutaraldehyde, washed, and stained 72 h at 37°C in PBS supplemented with 20 mM K3Fe(CN), 20 mM K4Fe(CN)6, 2 mM MgCl2, and 1 mg/mL X-gal. They were then washed and counterstained with Nuclear Fast Red. No staining was detected on sections from wild-type mice treated in the same conditions. A Leica SCN400 scanner acquired the pictures of complete sagittal brain sections.
+ Open protocol
+ Expand
2

Evaluating Liver Inflammation and Fibrosis in MDR2KO Mice

Check if the same lab product or an alternative is used in the 5 most similar protocols
In order to measure the amount of IBDM in wildtype and MDR2KO mice in the absence or presence of corticosterone, IHC on paraffin-embedded liver sections was performed using a CK19 antibody for labeling the cholangiocytes, followed by VectaStain ABC kit from Vector Laboratories Inc. (Burlingame, CA, USA) for color development, following previous described protocols [9 (link)]. Liver sections of 4 μm were obtained with a Leica microtome. The VectaStain-stained sections were mounted on slides, and scanned with a Leica SCN400 scanner, with 20× optical magnification. Screenshots with 10× digital magnification were taken and used for quantification of field-stained pixel percentage of CK19-positive cells. The same procedure was employed for IHC of CD68, F4/80, Clec4f, Ccr2 and αSMA in liver sections. The images were analyzed with ImageJ software downloaded from the NIH website. The degree of fibrosis in FVBN and MDR2KO mice treated with vehicle or corticosterone was assessed by staining collagen I and III fibers in liver sections with Sirius Red (kit from Sigma Aldrich, St. Louis, MO, USA) and then processing the slides in the same manner used for IHC analysis. Apoptosis in the liver of FVBN and MDR2KO mice was assessed using a TUNEL kit from Abcam (Cambridge, MA, USA) according to manufacturer’s instructions and was conterstained with methyl green.
+ Open protocol
+ Expand
3

Organ Fixation and Cryosectioning Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Organs from toxin challenged mice were fixed in 4% paraformaldehyde overnight, washed twice in PBS and then cryopreserved in 15% sucrose for three hours followed by 30% sucrose overnight. Organs were embedded in NEG 50, flash frozen in 2-methylbutane chilled with liquid nitrogen, and cryosectioned at 10 μm. The hematoxylin and eosin (H&E) stained sections were scanned at 40× magnification on a Leica SCN400 scanner for analysis.
+ Open protocol
+ Expand
4

Tissue Immunohistochemistry for Ki-67 and Sortilin

Check if the same lab product or an alternative is used in the 5 most similar protocols
Tissue sections were fixed with 4% phosphate-buffered formaldehyde, embedded in paraffin and cut into 4.5-μm-thick sections. Immunohistochemistry was performed using Dako Autostainer LINK 48 using Envision FLEX+ detection system (Dako, Glostrup, Denmark). Briefly, deparaffinized sections were subjected to antigen retrieval by high-pressure cooking and DIVA antigen retrieval pH 6.2, followed by blocking with 3% hydrogen peroxide and incubation with primary antibody against anti-Ki67 (monoclonal mouse anti-human Ki-67 antigen clone MIB-1. M7240 (Dako) and anti-sortilin antibody (polyclonal rabbit anti-sortilin, #AB16640, Abcam) at RT for 1 h. For signal amplification EnVision™ FLEX+ rabbit linker, SM805, (Dako) and EnVision™ FLEX+ mouse linker SM804 (Dako) was used, respectively. Further EnVision FLEX/HRP visualization reagent EnVision™ FLEX/HRP secondary antibody-coated polymer peroxidase complexes (#SM802, Dako), followed by DAB substrate/chromogen (Dako) was used. Slides were counterstained with Dako hematoxylin. Stained sections were scanned by Leica SCN400 scanner at 20× and evaluated by the automated image analysis Definiens Developer XD tissue studio program.
+ Open protocol
+ Expand
5

Histological Image Digitization and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Histological slides were digitized on LEICA SCN400 scanner (LEICA, Milton Keynes UK) at 40× magnification. Digital image analysis was performed on Definiens Developer 2.4 (Munich, Germany). Image analysis was done as previously published [6 (link)].
+ Open protocol
+ Expand
6

Histopathological Analysis of FFPE Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
Samples were formalin-fixed, paraffin-embedded (FFPE), sectioned and stained with haematoxylin-eosin (H&E) according to standard histopathological techniques. For immunohistochemistry, sections were incubated with anti-human CD166 (Novaocastra), E-cadherin (Epitomics) and metallothioneins (Dako), and visualized using the Envision HRP Polymer System (Dako). All images were captured on a high-throughput Leica SCN400 scanner.
+ Open protocol
+ Expand
7

Histological and Fluorescent Imaging Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Histological slides were digitised on a LEICA SCN400 scanner (LEICA UK) at 40× magnification and 65% image compression setting, and images were stored on Slidepath Digital Image Hub (Leica Microsystems). Fluorescent images were acquired on a ZEISS LSM710 META confocal laser scanning microscope and processed with the ZEN software.
X-Gal-stained frozen sections were captured prior to counterstaining on an Olympus MegaView III digital camera, attached to a Zeiss Axioskop and then counterstained with Nuclear Fast Red, and images were digitised on a LECIA SCN400 scanner.
+ Open protocol
+ Expand
8

Histological Slide Digitization and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Histological slides were digitised on LEICA SCN400 scanner (LEICA, Milton Keynes UK), or Hamamatsu S360 (Hamamatsu Welwyn Garden City, UK) at 40x magnification, and images were captured from the LECIA Slidepath slide management software. Digital image analysis was performed on Definiens Developer 2.4 (Munich, Germany) as previously published (17 (link),22 (link)) or on the open source software QuPath (23 (link)) Version 0.2m2.
+ Open protocol
+ Expand
9

Quantification of Macrophage and Inflammatory Markers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Macrophage and inflammation expression were evaluated by Immunohistochemical (IHC) analysis following a general IHC protocol. Tissue sections were immunostained at 4°C overnight with antibody against the macrophage marker RAM11 (DAKO, Santa Clara, CA, USA), or with antibodies against the inflammatory markers: TNF-α (ABCAM, Cambridge, United Kingdom), IL-1β (NOVUS, Littleton, CO, USA), or IL-6 (Santa Cruz Biotechnologies, CA, USA). The primary antibody was detected using a peroxidase-based kit (DAKO, Glostrup, Denmark), and visualized using 3,3′-diaminobenzidine substrate with enhancer (DAKO). The sections were subsequently counterstained with hematoxylin (DAKO). Digital images of the vessels were scanned using a SCN400 scanner (Leica), and histomorphometry was performed using LAS 4.2 software (Leica).
+ Open protocol
+ Expand
10

Evaluating Nuclear Positivity of MSH3

Check if the same lab product or an alternative is used in the 5 most similar protocols
Slides were evaluated and scored by an experienced pathologist for nuclear positivity of MSH3 (given as per cent, %) blinded to MSI and EMAST status of each case. A composite high-resolution image at 20× magnification of each slide was obtained with a Leica SCN400 scanner and uploaded onto an internal digital image hub for image analysis.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!