Hematoxylin and eosin (HE) staining (G1120, Solarbio, China), Safranin O-fast green (SO-FG) staining (Servicebio, China), and Sirius red staining (G1018, Servicebio, China) were carried out following the manufacturer's procedures. A Pannoramic MIDI scanner (3DHISTECH, Hungary) was used to capture images.
Pannoramic midi scanner
Manufactured by 3DHISTECH
Sourced in Hungary
The Pannoramic MIDI scanner is a high-speed digital slide scanning system designed for pathology laboratories. It captures digital images of glass slides, enabling digital pathology workflows. The scanner's core function is to digitize microscope slides for storage, analysis, and remote consultation.
Automatically generated - may contain errors
Lab products found in correlation
Caseviewer software, by 3DHISTECH (10 mentions)
Pannoramic viewer software, by 3DHISTECH (6 mentions)
Lsm 880, by Zeiss (4 mentions)
Caseviewer 2, by 3DHISTECH (4 mentions)
Fd rapid golgistain kit, by FD NeuroTechnologies (3 mentions)
Caseviewer, by 3DHISTECH (2 mentions)
4 6 diamidino 2 phenylindole (dapi), by Merck Group (2 mentions)
Aipathwell software, by Wuhan Servicebio Technology (2 mentions)
Superfrost plus slide, by Thermo Fisher Scientific (2 mentions)
G1018, by Wuhan Servicebio Technology (1 mentions)
G1120, by Solarbio (1 mentions)
Alexa fluor 488 conjugated goat anti mouse, by Thermo Fisher Scientific (1 mentions)
Dab substrate kit, by Beijing Strong Biotechnologies (1 mentions)
Rotary microtome, by Leica (1 mentions)
Nlrp1, by Santa Cruz Biotechnology (1 mentions)
Nissl staining solution, by Beyotime (1 mentions)
Image pro plus 6, by Media Cybernetics (1 mentions)
Application suite x microscope software, by Leica (1 mentions)
Huygens deconvolution software, by Scientific Volume Imaging (1 mentions)
Taz antibody, by Abcam (1 mentions)
84 protocols using pannoramic midi scanner
1
Histological Staining Protocols for Tissue Analysis
2
Quantifying Immunofluorescence Staining in Cells
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The MSK Molecular Cytology Core Facility performed CAV1 and HER2 immunofluorescence staining of formalin-fixed, paraffin-embedded sections (10 μM) sections. The whole slide digital images of HER2 and CAV1 staining were obtained on Pannoramic MIDI scanner (3DHistech, Hungary) at a resolution of 0.3250 μm per pixel. Regions of interest around the cells were then drawn and exported as.tif files from these scans using Caseviewer (3DHistech, Hungary.) These images were then analyzed using ImageJ/FIJI (NIH, USA) to measure fluorescence intensity after applying a median filter and background subtraction.
3
Placental MEM-G2 and CAM5.2 Staining
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We set out to compare the extent of MEM-G2 and CAM5.2 staining in term placentas between the study groups. All of the slides were scanned by a Pannoramic Midi scanner (version 11, 3DHISTECH, Budapest, Hungary). The entire decidua basalis was quantitatively analyzed using the HistoQuant modus in Quant Center software (version 2.1, 3DHISTECH). This was done by two investigators (JS and HK) independently for 10 placentas to analyze interobserver variability. For each staining, the same thresholds and training scenarios were used for patient and control slides. We corrected for the selected surface area when calculating the percentage positivity of a staining.
For first trimester material, we could not define the decidua. Therefore, we only analyzed the HLA-G positive parts of the slides. Scoring of the slides was performed by two investigators (JS and ME) independently, blinded for the cause of the abortion. Based on the extent of staining, cases were classified according to a semi-quantitative scoring system, i.e., (1) minimal, (2) moderate, or (3) intense staining. Examples of stainings are shown inFigure S1 .
For first trimester material, we could not define the decidua. Therefore, we only analyzed the HLA-G positive parts of the slides. Scoring of the slides was performed by two investigators (JS and ME) independently, blinded for the cause of the abortion. Based on the extent of staining, cases were classified according to a semi-quantitative scoring system, i.e., (1) minimal, (2) moderate, or (3) intense staining. Examples of stainings are shown in
4
Immunofluorescence Analysis of TNBC
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The TNBC tissue microarray was incubated with a specific primary antibody at 4 °C overnight. The cells were then incubated for 1 h with Alexa Fluor 488-conjugated goat anti-mouse and Alexa Fluor 647-conjugated donkey anti-rabbit secondary antibodies (Molecular Probes). Nuclei were counterstained with 0.1 μg/mL DAPI (Sigma). Total fluorescence intensity was examined and analyzed using the Pannoramic MIDI scanner from “3DHISTECH”.
5
Immunohistochemical Staining of HNSCC Samples
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Immunohistochemical staining was conducted as previously described [59 (link)]. Briefly, human and mouse HNSCC samples were paraffin embedded and sectioned at 4 μm. Following xylene deparaffinization and gradient ethanol soaking rehydration, the sections were subjected to high-temperature antigen retrieval with a citrate antigen retrieval solution and endogenous peroxidase inhibition with 3% hydrogen peroxide. Then, the non-specific binding was blocked using 5% goat serum (Mxb Biotechnologies, Fuzhou, China, KIT-9710). The processed sections were then incubated with primary antibodies (Table S2 ) at 4 °C overnight, washed with PBS, and incubated with horseradish peroxidase-conjugated secondary antibodies (Mxb Biotechnologies, KIT-9710) at 37 °C for 30 min. A DAB substrate kit (Mxb Biotechnologies, DAB-0031) and hematoxylin were used for staining. Images were visualized using a Pannoramic MIDI scanner (3DHISTECH) and quantified using the Aperio ScanScope software (v11.1.2.752, Aperio, San Diego, CA, USA). IgG was used as a negative control.
6
Digital Pathology Analysis Pipeline
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IHC stained slides were digitized with the whole-slide Pannoramic MIDI scanner (3DHISTECH Ltd., Budapest, Hungary) at 20× magnification. Digital image analysis was performed on whole sample areas, excluding only detected artefacts and folded and/or broken regions, which were considered uninformative. Ki67, SYP, KANK1, and DOCK8 were analyzed automatically using Pannoramic Viewer (PV) software (3DHISTECH), and their number of positive cells were determined by applying the NuclearQuant module. This module could be applied to non-nuclear stained samples by adjusting nucleus size settings to detect entire cells when required (nuclear radius 3–15 µm) and adjusting color deconvolution settings. HistoQuant module of PV was applied in VN-stained sections to obtain the areas of each VN intensity expression. All data obtained from PV modules were validated with pathologist’s morphological assessment of the digital image. Digitally obtained data and subsequent pathologist evaluation differed by only 5–10%.
7
CMNV Detection in M. rosenbergii Tissues
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Tissue samples of intestine, hepatopancreas, gill and gonad from partial CMNV-positive M. rosenbergii individuals which had been fixed in 4% PFA for 24 h, are dehydrated in a graded series of 70%, 85%, 90%, 95% and absolute ethanol, then processed and embedded in paraffin [26 ]. Two pieces of paraffin slices (3 µm) from each tissue samples were prepared using a rotary microtome (Leica, Wetzlar, Germany): one section was used for ISH detection [3 (link),14 (link),23 (link)]; another was stained with hematoxylin and eosin (H&E) as descripted elsewhere [27 ] for histopathological analysis. All slides of ISH and H&E were digitized with the whole-slide Pannoramic MIDI scanner (3DHISTECH Ltd., Budapest, Hungary) at 40× magnification.
8
Histological Analysis of Arthritic Mice
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Arthritic mice (selected from each experimental group based on similar arthritis score) were sacrificed, and their hind limbs were collected and processed using standard histological procedures. Sections were stained with Mayer’s hematoxylin and eosin (H&E) and scanned using Pannoramic MIDI Scanner (3DHistech, Hungary). Images were analyzed using the Pannoramic Viewer Software (3DHistech).
9
Immunohistochemical Analysis of mTOR and NLRP1
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Mice were deeply anaesthetized and transcardially perfused with 20 ml PBS followed by 20 ml of cold 4% paraformaldehyde (PFA). Brains (from 3 mice in each group) were then removed and post-fixed with the same 4% PFA solution for 4–6 h at 4 ℃. The samples were then transferred to 30% sucrose in PBS overnight. Sample Sects. (14 μm) were prepared on gelatin-coated glass slide via cryosection. The sections were then washed three times in PBS for 5 min each, blocked with 5% bovine serum albumin (BSA) and 0.2% Triton X-100 for 1 h at room temperature and then incubated with primary antibody against mTOR (CST, Beverly, MA, USA) or NLRP1 (Santa Cruz, CA, USA) at 4 °C overnight. After washing with phosphate-buffered solution (PBS), samples were incubated with appropriate secondary antibody at room temperature for 1 h and cell nuclei were stained with DAPI. Fluorescent images were captured with a Pannoramic MIDI scanner (3D HISTECH, Budapest, Hungary).
10
Nissl Staining of Hippocampus
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5-μm paraffin coronal sections of the hippocampus (from 3 mice in each group) were washed with distilled water and stained with Nissl staining solution (Beyotime, China), incubated for 5 min at 37 °C. Then, sections were washed twice with distilled water for a few seconds, rinsed with 95% ethanol for 5 min and air dry. Sections were washed twice in xylene for 5 min each. After sealing with neutral balsam, the stained sections were examined under a Pannoramic MIDI scanner (3D HISTECH, Budapest, Hungary). Nissl-positive cells were calculated by Image-Pro Plus 6.0 software (Media Cybernetics, USA) by a person blinded to group assignment. Results are expressed as relative numbers of neurons.
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