Axio scanner z1

Manufactured by Zeiss

Sourced in Germany

The Axio Scanner Z1 is a high-resolution scanning system designed for whole slide imaging. It captures digital images of entire microscope slides with a resolution of up to 0.22 micrometers per pixel. The system is equipped with an automated slide loader and advanced optics to provide consistent, high-quality digital scans.

Automatically generated - may contain errors

Lab products found in correlation

Serum free protein blocking solution, by Agilent Technologies (2 mentions) Opal multiplex system, by PerkinElmer (2 mentions) 4 6 diamidino 2 phenylindole (dapi), by Vector Laboratories (2 mentions) Zen blue lite software, by Zeiss (1 mentions) Ab75813, by Abcam (1 mentions) Pa5 16634, by Thermo Fisher Scientific (1 mentions) Fluoroshield mounting medium with dapi, by Abcam (1 mentions) Alexa fluor 594 donkey anti rat igg, by Thermo Fisher Scientific (1 mentions) Alexa fluor 647 donkey anti rabbit igg, by Jackson ImmunoResearch (1 mentions) Axio imager m2, by Zeiss (1 mentions) Zen microscope software, by Zeiss (1 mentions) Axio observer 7, by Zeiss (1 mentions) Agarose, by Merck Group (1 mentions) Zen 2 blue edition software, by Zeiss (1 mentions) Pk 4000, by Vector Laboratories (1 mentions) Ba 7000, by Vector Laboratories (1 mentions) Sk 4100, by Vector Laboratories (1 mentions) Axioobserver z1 light, by Zeiss (1 mentions) Zen blue software, by Zeiss (1 mentions) Lsm 780 confocal microscope, by Zeiss (1 mentions)

Close spelling variants of this product

Zeiss Axio Scan Z1 slide scanner fluorescence microscope Axio Scan.Z1 scanner Axio Scan Z1 automated slide scanner Axio Scan.Z1 Slide Scanner microscope Axio Scan.Z1 slide scanner Axio Scan Z1 Brightfield/Fluorescence Slide Scanner Axio Scan.Z1 Digital Slide Scanner

14 protocols using axio scanner z1

Ovarian Follicle Quantification Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

Ovaries were dissected and placed in 4% formaldehyde (Chek1 cKO (Ddx4)) & Bouin’s fixative solution (70% saturated picric acid solution (Applichem, A2520, 1000), 25% formaldehyde, 5% glacial acetic acid (Merck, 1.00063.2500)) or 4% formaldehyde for Chek1 cKO (Ddx4-Cre) overnight at 4 °C. The ovaries were washed two times with cold PBS for 30 minutes followed by dehydration with an increasing concentration of ethanol. Subsequently, the samples were submerged in Histo-Clear II (Cat. # HS-202, National Diagnostics) for 30 min. at room temperature. This was repeated another two times (three times in total) with fresh Histo-Clear II. Ovaries were embedded in paraffin blocks and cut to a thickness of 7 μm (sCHEK1 and Chek2) and 6 μm (Chek1 cKO (Ddx4-Cre)) and mounted on poly-L-lysine coated slides. After de-paraffinization and rehydration, the slides were stained with PAS-hematoxylin. The tissue was imaged using a Zeiss Axio scanner Z.1 and follicles with a visible nucleus were counted using the Zen Blue lite software from Zeiss. Primordial follicles contain one layer of flat granulosa cells surrounding the oocytes, primary follicles have one layer of cuboid granulosa cells. Secondary follicles contain two or more layers of granulosa cells and antral follicles are those with one or several cavities (the antrum).

Ruth K.S., Day F.R., Hussain J., Martínez-Marchal A., Aiken C.E., Azad A., Thompson D.J., Knoblochova L., Abe H., Tarry-Adkins J.L., Gonzalez J.M., Fontanillas P., Claringbould A., Bakker O.B., Sulem P., Walters R.G., Terao C., Turon S., Horikoshi M., Lin K., Onland-Moret N.C., Sankar A., Hertz E.P., Timshel P.N., Shukla V., Borup R., Olsen K.W., Aguilera P., Ferrer-Roda M., Huang Y., Stankovic S., Timmers P.R., Ahearn T.U., Alizadeh B.Z., Naderi E., Andrulis I.L., Arnold A.M., Aronson K.J., Augustinsson A., Bandinelli S., Barbieri C.M., Beaumont R.N., Becher H., Beckmann M.W., Benonisdottir S., Bergmann S., Bochud M., Boerwinkle E., Bojesen S.E., Bolla M.K., Boomsma D.I., Bowker N., Brody J.A., Broer L., Buring J.E., Campbell A., Campbell H., Castelao J.E., Catamo E., Chanock S.J., Chenevix-Trench G., Ciullo M., Corre T., Couch F.J., Cox A., Crisponi L., Cross S.S., Cucca F., Czene K., Smith G.D., de Geus E.J., de Mutsert R., de Vivo I., Demerath E.W., Dennis J., Dunning A.M., Dwek M., Eriksson M., Esko T., Fasching P.A., Faul J.D., Ferrucci L., Franceschini N., Frayling T.M., Gago-Dominguez M., Mezzavilla M., García-Closas M., Gieger C., Giles G.G., Grallert H., Gudbjartsson D.F., Gudnason V., Guénel P., Haiman C.A., Håkansson N., Hall P., Hayward C., He C., He W., Heiss G., Høffding M.K., Hopper J.L., Hottenga J.J., Hu F., Hunter D., Ikram M.A., Jackson R.D., Joaquim M.D., John E.M., Joshi P.K., Karasik D., Kardia S.L., Kartsonaki C., Karlsson R., Kitahara C.M., Kolcic I., Kooperberg C., Kraft P., Kurian A.W., Kutalik Z., Bianca M.L., LaChance G., Langenberg C., Launer L.J., Laven J.S., Lawlor D.A., Marchand L.L., Li J., Lindblom A., Lindstrom S., Lindstrom T., Linet M., Liu Y., Liu S., Luan J., Mägi R., Magnusson P.K., Mangino M., Mannermaa A., Marco B., Marten J., Martin N.G., Mbarek H., McKnight B., Medland S.E., Meisinger C., Meitinger T., Menni C., Metspalu A., Milani L., Milne R.L., Montgomery G.W., Mook-Kanamori D.O., Mulas A., Mulligan A.M., Murray A., Nalls M.A., Newman A., Noordam R., Nutile T., Nyholt D.R., Olshan A.F., Olsson H., Painter J.N., Patel A.V., Pedersen N.L., Perjakova N., Peters A., Peters U., Pharoah P.D., Polasek O., Porcu E., Psaty B.M., Rahman I., Rennert G., Rennert H.S., Ridker P.M., Ring S.M., Robino A., Rose L.M., Rosendaal F.R., Rossouw J., Rudan I., Rueedi R., Ruggiero D., Sala C.F., Saloustros E., Sandler D.P., Sanna S., Sawyer E.J., Sarnowski C., Schlessinger D., Schmidt M.K., Schoemaker M.J., Schraut K.E., Scott C., Shekari S., Shrikhande A., Smith A.V., Smith B.H., Smith J.A., Sorice R., Southey M.C., Spector T.D., Spinelli J.J., Stampfer M., Stöckl D., van Meurs J.B., Strauch K., Styrkarsdottir U., Swerdlow A.J., Tanaka T., Teras L.R., Teumer A., Porsteinsdottir U., Timpson N.J., Toniolo D., Traglia M., Troester M.A., Truong T., Tyrrell J., Uitterlinden A.G., Ulivi S., Vachon C.M., Vitart V., Völker U., Vollenweider P., Völzke H., Wang Q., Wareham N.J., Weinberg C.R., Weir D.R., Wilcox A.N., van Dijk K.W., Willemsen G., Wilson J.F., Wolffenbuttel B.H., Wolk A., Wood A.R., Zhao W., Zygmunt M., Chen Z., Li L., Franke L., Burgess S., Deelen P., Pers T.H., Grøndahl M.L., Andersen C.Y., Pujol A., Lopez-Contreras A.J., Daniel J.A., Stefansson K., Chang-Claude J., van der Schouw Y.T., Lunetta K.L., Chasman D.I., Easton D.F., Visser J.A., Ozanne S.E., Namekawa S.H., Solc P., Murabito J.M., Ong K.K., Hoffmann E.R., Murray A., Roig I, & Perry J.R. (2021). Genetic insights into biological mechanisms governing human ovarian ageing. Nature, 596(7872), 393-397.

+ Open protocol

+ Expand

Skeletal Muscle Biopsy and Immunostaining

Check if the same lab product or an alternative is used in the 5 most similar protocols

Skeletal muscle biopsies were collected from semimembranosus, vastus lateralis and gastrocnemius muscles on day 28 post occlusion in formalin. A systematic approach was followed to collect biopsies from 3 different parts (proximal, middle, and distal) of each muscle to show heterogeneity. Paraffin embedded samples were processed as previously described^{58 (link)}. Briefly, the tissue sections (8 µm thick) were stained with hematoxylin for 5 min, washed in PBS and then counterstained with eosin for 2 min. The sections were dehydrated with graded alcohol and washed with xylene followed by mounting. For immunostaining, sodium citrate (pH 6.0) antigen retrieval, blocking with 10% normal goat serum at room temperature was performed, then incubated with rat laminin ab (MA1-06100; 1:200; ThermoFisher), rabbit vWF (PA5-16634; 1:200; ThermoFisher), rabbit NCAM1 ab (ab75813; 1:1000; abcam) and mouse MYH1 ab (67299-1-IG; 1:1000; ThermoFisher) overnight at 4 °C. Signal was visualized by subsequent fluorescence-tagged secondary antibodies (Alexa Fluor 488-tagged α-rat, 1:200, Alexa Fluor 568-tagged α-rabbit, 1:200, and Alexa Fluor 488-tagged α-mouse, 1:200) respectively with DAPI counterstained. Images were collected using Axioscanner Z1 (Zeiss).

El Masry M.S., Gnyawali S.C, & Sen C.K. (2023). Robust critical limb ischemia porcine model involving skeletal muscle necrosis. Scientific Reports, 13, 11574.

+ Open protocol

+ Expand

Quantifying α-Klotho Protein Levels in Mouse Brain

Check if the same lab product or an alternative is used in the 5 most similar protocols

Stained α-Klotho mouse whole brain sections were scanned using an Axio Scanner Z1 (Zeiss) at 20x magnification. Photoshop CC 19.1 (Adobe, Inc.) was used to virtually dissect the choroid plexus, whole cerebellum, and background samples, avoiding major blood vessels with erythrocytes or tissue folding that could interfere with fluorescence intensity calculations. Using ImageJ FIJI,⁵⁴ (link) the region of interest (ROI) was selected for analysis to exclude blood vessels and folding of tissue that can interfere with intensity measurements. ROI areas were quantified for raw intensity and then corrected with background on the same section. Results are shown as the corrected mean intensity, calculated as corrected intensity divided by area.

Zhu Y., Prata L.G., Gerdes E.O., Netto J.M., Pirtskhalava T., Giorgadze N., Tripathi U., Inman C.L., Johnson K.O., Xue A., Palmer A.K., Chen T., Schaefer K., Justice J.N., Nambiar A.M., Musi N., Kritchevsky S.B., Chen J., Khosla S., Jurk D., Schafer M.J., Tchkonia T, & Kirkland J.L. (2022). Orally-active, clinically-translatable senolytics restore α-Klotho in mice and humans. EBioMedicine, 77, 103912.

+ Open protocol

+ Expand

Immunofluorescent Analysis of Lacrimal Glands

Check if the same lab product or an alternative is used in the 5 most similar protocols

At the end of the study, lacrimal glands were excised from the mice. Lacrimal glands were fixed with 4% PFA overnight, followed by cryoprotection through incubation in 30% sucrose overnight, and lastly embedded in O.C.T. medium. The cyrosections were obtained at 7 μm thick and stained with fluorescent antibodies. Specifically, 7 μm sections were blocked with 5% normal donkey serum and 1% Tween20 in PBS. Blocked sections were incubated overnight at 4 °C with rat anti-FoxP3 (FJK-16s; eBio) and rabbit anti-CD3 (SP7, monoclonal rabbit IgG; Abcam, Cambridge, MA). The sections were then incubated with a secondary antibody, Alexa Fluor 594 donkey anti-rat IgG (ThermoFisher Scientific Waltham, MA) and Alexa Fluor 647 donkey anti-rabbit IgG (Jackson ImmunoResearch Laboratories, West Grove, PA) for 1 hour at room temperature and then mounted using Fluoroshield mounting medium with DAPI (Abcam, Cambridge, MA). The images were captured using a Zeiss Axio Scanner Z.1. Only positively stained cells overlapping DAPI (nuclei) were quantified.

Ratay M.L., Balmert S.C., Acharya A.P., Greene A.C., Meyyappan T, & Little S.R. (2017). TRI Microspheres prevent key signs of dry eye disease in a murine, inflammatory model. Scientific Reports, 7, 17527.

+ Open protocol

+ Expand

Automated Brain Imaging Workflow

Check if the same lab product or an alternative is used in the 5 most similar protocols

Images were obtained at 10× with either the Zeiss AxioImager M2, Zeiss AxioScanner Z1 or Zeiss AxioObserver 7 microscopes. Entire brain sections were tiled using motorized stage controls and stitched using Zeiss ZEN Microscope Software.

Lee C., Côté S.L., Raman N., Chaudhary H., Mercado B.C, & Chen S.X. (2023). Whole-brain mapping of long-range inputs to the VIP-expressing inhibitory neurons in the primary motor cortex. Frontiers in Neural Circuits, 17, 1093066.

+ Open protocol

+ Expand

Comet Assay for DNA Damage Assessment

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Exponentially growing cells cultured in 6-well plates were irradiated with 8 Gy photon or proton irradiation. Alkaline buffers were prepared according to [61 (link)]. Cells were collected at defined time points after irradiation (30 min, 4 h, 8 h, 24 h) by trypsinization. The cell suspension (100 μL) was mixed with 200 μL agarose (40 °C, 1% in ddH₂O, low melting, Sigma-Aldrich, Deisenhofen, Germany) and pipetted onto an agarose-precoated slide. The agarose clot was covered with a cover slip, which was removed after solidification of the agarose and subsequently placed in alkaline lysis buffer (pH > 13.0) for 1 h. The slides were then placed in alkaline electrophoresis buffer (pH > 12.3) for 10 min to allow buffer exchange prior to electrophoresis for 1 h (0.75 V/cm electrode distance). Subsequently, the slides were transferred in ddH2O for 10 min and allowed to air-dry overnight at room temperature. For fluorescence microscopy, propidium iodide solution (50 μg/mL in ddH2O) was added onto the dried slide and sealed with a cover slip. The comets were imaged by the Axio Scanner Z.1 with 10× objective magnification and using the ZEN 2 Blue edition software (Carl Zeiss AG, Germany) and the tail length determined with ImageJ (1.51j8 available at https://imagej.nih.gov/ij/; U.S. National Institutes of Health, Bethesda, MD, USA) and the plugin OpenComet (OpenComet v1.3.1) [62 (link)].

Szymonowicz K., Krysztofiak A., van der Linden J., Kern A., Deycmar S., Oeck S., Squire A., Koska B., Hlouschek J., Vüllings M., Neander C., Siveke J.T., Matschke J., Pruschy M., Timmermann B, & Jendrossek V. (2020). Proton Irradiation Increases the Necessity for Homologous Recombination Repair Along with the Indispensability of Non-Homologous End Joining. Cells, 9(4), 889.

+ Open protocol

+ Expand

Insulin Quantification in Mouse Pancreas

Check if the same lab product or an alternative is used in the 5 most similar protocols

The fixated pancreases were dehydrated in ethanol, cleared in xylene and embedded in paraffin. The paraffin blocks were cut in 4 µm sections, using a microtome. The sections were transferred to slides, dewaxed in Histolab-Clear (Histolab Products AB, #14250) and rehydrated in graded dilutions of alcohol (70–99%) in tap water. The slides were stained for insulin using a primary in-house antibody (Insulin 2006-4). The signal was amplified by a biotinylated secondary antibody, goat anti-guinea pig (BA-7000, Vector Laboratories, Newark, CA, USA), followed by peroxidase (ABC) (PK-4000, Vector Laboratories). Finally, the reaction was developed by the use of 3,3–diaminobenzidine (SK-4100, Vector Laboratories), and counterstaining was performed with a Hematoxylin Mayer solution (RH-pharmacy, #854183). The slides were examined and photographed using the Zeiss Axio Scanner Z1. The islet area (percent insulin-positive tissue relative to total tissue area) and insulin intensity were quantified using the QuPath software (version0.3.2) Pancreases from three mice per group were analyzed. Three sections per mice were quantified and the average was calculated.

Pedersen S.S., Prause M., Sørensen C., Størling J., Moritz T., Mariño E, & Billestrup N. (2023). Targeted Delivery of Butyrate Improves Glucose Homeostasis, Reduces Hepatic Lipid Accumulation and Inflammation in db/db Mice. International Journal of Molecular Sciences, 24(5), 4533.

+ Open protocol

+ Expand

Profiling Circulating Tumor and Hybrid Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

PBMCs were isolated from peripheral blood using density centrifugation with Ficoll-Paque PLUS as previously described and resuspended in FACS Buffer. Cells were then adhered to poly-d-lysine-coated slides through incubation at 37 °C for 15 min, permeabilized with Triton-X, and fixed with 4% PFA. Slides were stained with antibodies directed at cancer-specific antigens and CD45 (Table S3) and with DAPI. Slides were imaged using a Zeiss AxioObserver.Z1 light microscope, digitally scanned with a Zeiss AxioScanner.Z1, and analyzed using Zeiss Zen blue software (Carl Zeiss AG, Germany.)
Manual quantification was performed for randomly selected slide regions containing > 50,000 nuclei by individuals blinded to the clinical status of the patients or healthy controls. Thresholds for positivity were set off histograms of the unstained portions of the slides. Cells with DAPI nuclear staining were evaluated for CD45, CK, GFAP, CHGA/SYP status. At least 50,000 cells per patient were enumerated. CTCs were defined as tumor-marker (CK, GFAP, CHGA/SYP) positive, CD45 negative. CHCs were defined as cells with both tumor-marker and CD45 staining. Enumerated cells were normalized to 50,000 nuclei.

Dietz M.S., Sutton T.L., Walker B.S., Gast C.E., Zarour L., Sengupta S.K., Swain J.R., Eng J., Parappilly M., Limbach K., Sattler A., Burlingame E., Chin Y., Gower A., Mira J.L., Sapre A., Chiu Y.J., Clayburgh D.R., Pommier S.J., Cetnar J.P., Fischer J.M., Jaboin J.J., Pommier R.F., Sheppard B.C., Tsikitis V.L., Skalet A.H., Mayo S.C., Lopez C.D., Gray J.W., Mills G.B., Mitri Z., Chang Y.H., Chin K, & Wong M.H. (2021). Relevance of circulating hybrid cells as a non-invasive biomarker for myriad solid tumors. Scientific Reports, 11, 13630.

+ Open protocol

+ Expand

Immunohistochemistry of FFPE Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols

FFPE sections were used for all IHC experiments. Antigen retrieval was performed by heat-induced epitope retrieval using citrate buffer (pH6), Tris/EDTA (pH9), or proteinase K treatment. After blocking with serum-free protein blocking solution (Dako), slides were incubated for primary antibodies for 1 hr at RT, a secondary Ab for 30 min at RT, and then subjected to Fast Red or DAB chromogen development. The details of antibodies are shown in Supplementary Table 3. Slides were then counterstained with hematoxylin, dehydrated, and mounted. Stromal content and acinar cells were assessed by Movat’s pentachrome staining following the manufacturer’s protocol (modified according to Verhoeff, Morphisto GmbH, Germany).
Slides were scanned and digitalized by Zeiss AxioScanner Z.1 (Carl Zeiss AG, Germany) with ×10 objective magnification. The percentage of positive cells for IHC staining was quantified by Definiens (Definiens AG, Germany). For quantification, the total number of cells of the whole-tissue section was measured based on nuclei staining (hematoxylin) detected by the software (Supplementary Fig. 11).

Cheung P.F., Yang J., Fang R., Borgers A., Krengel K., Stoffel A., Althoff K., Yip C.W., Siu E.H., Ng L.W., Lang K.S., Cham L.B., Engel D.R., Soun C., Cima I., Scheffler B., Striefler J.K., Sinn M., Bahra M., Pelzer U., Oettle H., Markus P., Smeets E.M., Aarntzen E.H., Savvatakis K., Liffers S.T., Lueong S.S., Neander C., Bazarna A., Zhang X., Paschen A., Crawford H.C., Chan A.W., Cheung S.T, & Siveke J.T. (2022). Progranulin mediates immune evasion of pancreatic ductal adenocarcinoma through regulation of MHCI expression. Nature Communications, 13, 156.

+ Open protocol

+ Expand

Confocal Microscopy for Tissue Imaging

Check if the same lab product or an alternative is used in the 5 most similar protocols

Immunofluorescent imaging was performed using a Zeiss LSM 780 Confocal Microscope (Carl Zeiss, Germany) with a motorized stage using Zeiss Zen (v2, blue edition) software. Whole transverse sections were imaged using a Plan Apochromat 20x/0.8 M27 objective. Light microscopy was performed using a Zeiss Axio Scanner Z1 (Carl Zeiss, Germany) with the Zen (v2, Blue edition) software. All sections on the slide were scanned using the automated tissue detector feature in Zen (v2, blue edition) software.

Siddiqui A.M., Thiele F., Stewart R.N., Rangnick S., Weiss G.J., Chen B.K., Silvernail J.L., Strickland T., Nesbitt J.J., Lim K., Schwarzbauer J.E., Schwartz J., Yaszemski M.J., Windebank A.J, & Madigan N.N. (2023). Open-Spaced Ridged Hydrogel Scaffolds Containing TiO2-Self-Assembled Monolayer of Phosphonates Promote Regeneration and Recovery Following Spinal Cord Injury. International Journal of Molecular Sciences, 24(12), 10250.

+ 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?

Revolutionizing how scientists
search and build protocols!