For imaging the growth of C. albicans in different organs, mice were infected with prelabeled C. albicans, either with 0.05% Uvitex 2B or 10 μg/ml FITC. The labeled fungi were injected via the tail vein at a concentration of 106 per mouse. At designated times, the kidneys and brain were collected and directly imaged using an inverted confocal microscope (Zeiss LSM800) with a 63x objective for the highest resolution. The images were analyzed using ZEISS ZEN 3.0 (blue edition) software. Z projection images were generated for organ imaging. In cases where confocal microscopy was not feasible for imaging large quantities, an inverted Nikon Ti2 microscope was used, and the images were analyzed using FIJI software.
Zen 3.0 blue edition software
Manufactured by Zeiss
Sourced in Germany
ZEN 3.0 (blue edition) is a software suite developed by Zeiss for microscopy and imaging applications. It provides a unified interface to control and operate various Zeiss microscope models and imaging systems. The software enables users to capture, process, and analyze digital images and data obtained from Zeiss microscopes.
Automatically generated - may contain errors
Lab products found in correlation
Axiocam 105, by Zeiss (2 mentions)
Axio observer microscope, by Zeiss (2 mentions)
Lsm 800, by Zeiss (1 mentions)
Ti2 microscope, by Nikon (1 mentions)
Axio imager z2 microscope, by Zeiss (1 mentions)
Permount, by Thermo Fisher Scientific (1 mentions)
Axiocam 506 camera, by Zeiss (1 mentions)
Lsm 800 confocal laser scanning microscope, by Zeiss (1 mentions)
Araldite, by Electron Microscopy Sciences (1 mentions)
Tissue tek oct compound, by Sakura Finetek (1 mentions)
Formalin, by Thermo Fisher Scientific (1 mentions)
Mirax scanner, by Zeiss (1 mentions)
2 methylbutane, by Thermo Fisher Scientific (1 mentions)
Prolong gold, by Thermo Fisher Scientific (1 mentions)
Tissue freezing medium, by Leica (1 mentions)
Axio scan z1, by Zeiss (1 mentions)
Filmtracer live dead biofilm viability kit, by Thermo Fisher Scientific (1 mentions)
Filmtracer sypro ruby biofilm matrix stain, by Thermo Fisher Scientific (1 mentions)
Dapi nucleic acid stain, by Thermo Fisher Scientific (1 mentions)
Sterile glass coverslips, by Hampton Research (1 mentions)
14 protocols using zen 3.0 blue edition software
1
Visualizing Candida albicans Organ Colonization
2
Embryo Sectioning and Imaging Protocol
3
Measuring CPTBCI Focus in Patients
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
At each of the four checkups, the CPTBCI focus surface area was measured for each CPTBCI case, and every patient completed the COMQ-12 (Phillips et al., 2014 (link)). The latter was validated and cross-culturally adapted in the target language (Vozel et al., 2020c (link)).
The CPTBCI foci (e.g., granulation tissue, redness, and edema) were detected and photographed by the leading researchers (DV and SB) with a diagnostic otomicroscope (OPMI pico/S100, Carl Zeiss Surgical GmbH, Oberkochen, Germany) at 5.1× and 8.5× magnification, for which calibration was performed. The focus of inflammation was instantly anatomically classified (Supplementary Material 2 ). Later, the independent blinded outcome assessor (NS), unaware of treatment allocation, outlined the focus and measured the CPTBCI focus surface using the ZEN 3.0 blue edition software (© Carl Zeiss Microscopy GmbH, 2019). Areas in mm2 were converted into a percentage with respect to the baseline CPTBCI surface area (i.e., 100% at the first checkup) as depicted in Figure 2 .
The CPTBCI foci (e.g., granulation tissue, redness, and edema) were detected and photographed by the leading researchers (DV and SB) with a diagnostic otomicroscope (OPMI pico/S100, Carl Zeiss Surgical GmbH, Oberkochen, Germany) at 5.1× and 8.5× magnification, for which calibration was performed. The focus of inflammation was instantly anatomically classified (
4
Histopathological Analysis of Aortic Valves
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Paraffin sections of hearts and lungs (4‐µm slices) were processed for immunohistochemistry. Whole hearts of neonatal pups, C57BL/6J mice, and NZO mice in the 22nd week of age were harvested for histopathological examination of AoVs in short‐axis view. Samples were fixed for 24 hours in 4% formalin (Thermo Scientific, Waltham, MA) and stored in 70% ethanol. After microdissection of aortic roots, tissue samples were embedded in Tissue‐Tek OCT compound (Sakura Finetek, Alphen aan den Rijn, the Netherlands), frozen in 2‐methylbutane (Thermo Scientific), cooled with dry ice, and sectioned into 6‐μm slices. Special care was taken that AoVs were kept intact to ensure best quality for histological analyses. Samples were stained with hematoxylin and eosin to visualize anatomic and morphologic structure of AoVs. Longitudinal cross‐sections of AoVs from C57BL/6J and NZO mice were used for picrosirius red, Alizarin red, and Movat pentachrome staining. For overview images, longitudinal and cross‐sectional heart slides and lungs were scanned using a MIRAX scanner (Zeiss, Ulm, Germany), which allows us to obtain digitized images of whole stained organ sections (scale, 2 mm). Quantification of images was performed using the image analysis tool from Zeiss ZEN 3.0 (blue edition) software, calculating the tissue area in pixel² and the percentage of stained area from total tissue area.
5
Analysis of Cryosectioned Tissue Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DLNs were obtained at different times postinoculation and frozen in tissue freezing medium (Leica, IL, USA) with liquid nitrogen and stored at -70°C until use. 5 μm cryosections were mounted on poly-L-lysine charged slides and fixed in cold acetone for 20 min and stored at -20°C after air-drying. Slides were rehydrated in wash buffer (PBS-0.5% saponin), blocked with 1% BSA in PBS, and incubated 1 hour with primary or fluorochrome-conjugated anti-mouse antibodies (detailed in supplemental Table 1 ). After two washing steps, secondary antibodies were incubated 1 h at room temperature. Relevant controls were run alongside. Slides were washed 3 times with wash buffer and mounted in antifade mounting medium (ProLong Gold; Invitrogen). Images were acquired with a Zeiss Axio Scan.Z1 slide scanner (Zeiss, Oberkochen, Germany) using a 20x objective and analyzed with Zen 3.0 Blue edition software (Carl Zeiss Microscopy, Jena, Germany).
6
Dual-species Biofilm Microscopy Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For microscopy, dual-species biofilms (Pseudomonas-Staphylococcus) were preformed on a glass. Sterile glass coverslips (Hampton Research, Aliso Viejo, CA, USA) were plunged in Petri dishes containing the bacterial cultures mixture 1:1 (v/v) in TSB with approximately 106 CFU/mL of each strain. The dishes were incubated at 37 °C for 48 h without shaking. Slides were carefully washed with sterile water, and then, 10 μL of SiL-gel or the vehicle gel (Alg-base) was dropped onto the slides, and they were incubated for 2 h at room temperature. Afterward, the slides were again carefully washed with sterile water two times.
Air-dried slides were stained with a 0.1% crystal violet solution for 15 min at RT, rinsed with water, and air-dried for bright-field microscopy. Other slides were stained with the DAPI Nucleic Acid Stain (Molecular Probes, Invitrogen, Eugene, OR, USA), the FilmTracer™ SYPRO® Ruby Biofilm Matrix Stain (Molecular Probes, Invitrogen, Eugene, OR, USA), and the FilmTracer™ LIVE/DEAD® Biofilm Viability Kit (Molecular Probes, Invitrogen, Eugene, OR, USA), according to the manufacturers’ instructions for dark-field fluorescent microscopy. All slides were imaged with the Axiostar Plus Transmitted Light Microscope (Zeiss AG, Jena, Germany) at ×400 and ×630 magnification. Microphotographs were proceeded with the ZEN 3.0 (blue edition) software (Zeiss AG, Jena, Germany).
Air-dried slides were stained with a 0.1% crystal violet solution for 15 min at RT, rinsed with water, and air-dried for bright-field microscopy. Other slides were stained with the DAPI Nucleic Acid Stain (Molecular Probes, Invitrogen, Eugene, OR, USA), the FilmTracer™ SYPRO® Ruby Biofilm Matrix Stain (Molecular Probes, Invitrogen, Eugene, OR, USA), and the FilmTracer™ LIVE/DEAD® Biofilm Viability Kit (Molecular Probes, Invitrogen, Eugene, OR, USA), according to the manufacturers’ instructions for dark-field fluorescent microscopy. All slides were imaged with the Axiostar Plus Transmitted Light Microscope (Zeiss AG, Jena, Germany) at ×400 and ×630 magnification. Microphotographs were proceeded with the ZEN 3.0 (blue edition) software (Zeiss AG, Jena, Germany).
7
Imaging Differentiating Hematopoietic Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cytospins were prepared and stained as previously described [60 (link)]. Images were collected using a Zeiss Primovert with an x40 objective and the Axiocam 105 color camera using ZEN 3.0 blue edition software (all Carl Zeiss AG, Oberkochen, Germany) at a resolution of 2560 x 1920 pixels. Differentiation marker CD14 was detected using anti-CD14-Alexa Fluor 700 antibody (clone HCD14, BioLegend, San Diego, CA, USA) as previously described [6 (link)].
8
Cytospins and Microscopic Imaging
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cytospins were performed as previously described [14 (link)]. Images were collected using a Zeiss Primovert microscope with an ×40 objective and the Axiocam 105 color camera using ZEN 3.0 blue edition software (all Carl Zeiss AG, Oberkochen, Germany) at a resolution of 2560 × 1920 pixels.
9
Immunofluorescence Staining of Mouse Lungs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Mouse lungs were fixed by transcardial and lung perfusion fixation. Mouse airways were embedded in paraffin, and tissue sections (5 µm) were stained using the standard protocol for immunofluorescence. CD44 and CLCA1 were detected using rat anti-CD44 conjugated with PE-Cyanine7 (Invitrogen, Dreieich, Germany) and rabbit anti-mouse Clca3 antibody (ab46512, Abcam, Berlin, Germany), respectively. The nucleus was counterstained with 5 µM Hoe33342 (Thermo Fisher Scientific, Darmstadt, Germany). Immunofluorescence was detected with an Axio Observer microscope equipped with Axiocams 503 mono, ApoTome.2, and ZEN 3.0 (blue edition) software (Zeiss, Oberkochen, Germany). Stitching microscopy was performed using a motorized Axio Observer and Zen software [40 (link)].
10
Lateral Imaging of Larval Gut
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Larvae are mounted lateral side down in 1% low gelling temperature agarose dissolved in PBS, over glass bottom culture dishes and overlaid with PBS for imaging. Use a flexible Eppendorf Microloader Pipette Tip to orient larvae in a lateral position for better visualization of fluorescent reporter expression. Z-stack acquisition is performed with Zeiss Zen 3.0 (blue edition) software for multipositions in an automated and motorized inverted microscope (Zeiss Axio Observer) using a 10× objective (NA 0.3) and a mercury lamp. Position the larvae to have the more distal part of the intestine centered anterior posteriorly and dorsal ventrally in the image. Set the lumen of the gut as the z-center level. Image each larva in the channels brightfield and mCherry (ex: 585 nm, em: 610 nm band pass filters) in 49 focal planes (149 μm range; 3 μm z step) so that all the gut depth is visible.
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
Revolutionizing how scientists
search and build protocols!