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Zen 2007

Manufactured by Zeiss
Sourced in Germany, United States

The Zen 2007 software is a microscope control and image processing platform developed by ZEISS. It provides a user-friendly interface for the operation and management of ZEISS microscope systems. The software enables the acquisition, processing, and analysis of microscopic images.

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7 protocols using zen 2007

1

Immunofluorescence Staining Protocol for Cells

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For immunofluorescence (IF), HeLa cells were grown on 12-mm coverslips at an initial density of 2.5 × 105 per well on 6-well plates. At 48 h after transfection, cells were fixed with 4% PFA in phosphate-buffered saline (PBS) for 15 min at room temperature (RT), permeabilized with 0.5% Triton X-100 in PBS (v/v) for 5 min at 4 °C, and blocked with 1% FBS in PBS (for 30 min at RT). All wash steps were done with PBS.
Primary antibodies were used for overnight incubation at 4 °C and secondary antibodies for 60 min at RT. DNA was stained with DAPI (4,6-diamidino-2-phenylindole, 0.2 μg/mL in mounting medium with Mowiol and DABCO). For imaging, the confocal microscopes LSM 510 META with the FCS system and Olympus FluoView FV1000 were used. Any brightness and contrast adjustments were performed in Adobe Photoshop, Zen 2007 (Carl Zeiss, Oberkochen, Germany) or ImageJ [64 (link)].
The fibroblasts were seeded on 12-mm coverslips to obtain 50% confluence, then fixed after 24 h and stained as described for HeLa cells. For imaging, the confocal microscope Leica SP8 (Leica Camera AG, Wetzlar, Germany) with LasX software was used. Z-stacks were presented as maximum intensity projection images.
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2

Confocal Laser Imaging of Imprints

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Imprints were analyzed by confocal laser scanning microscopy using LSM 510 META (Plan-Apochromat 63×, NA 1.4 oil immersion objective lens; Carl Zeiss Microimaging Inc., Thornwood, NY, USA). Laser lines used were at 488 nm, 543 nm, and 633 nm to excite fluorescein, rhodamine, and TO-PRO-3, respectively. Each dye was scanned in sequential mode to prevent fluorescence crosstalk. Acquisition software used was ZEN 2007 (Carl Zeiss Microimaging Inc.).
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3

Confocal and Fluorescence Microscopy Imaging

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For imaging, confocal microscope LSM 510 META with FCS system was used. For imaging in non-confocal mode, fluorescence microscope (Olympus IX70) was used. Any brightness and contrast adjustments were performed in Adobe Photoshop, Zen 2007 (Zeiss) or ImageJ (Schneider et al. 2012 (link)).
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4

Immunofluorescent Staining of Bone Sections

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Slides from WT and GIT1 KO femure fractures were deparaffinized in xylene, rehydrated in graded ethanol, and rinsed in distilled, deionized H2O as described above. For PECAM1 (CD31) detection, slides were boiled for 15 minutes in citrate buffer (Zymed Laboratories, San Francisco, CA), cooled for 20 minutes, and washed in PBS for 5 minutes. Slides were then blocked with normal goat serum containing 5% BSA in PBS for 30–60 minutes and incubated overnight with primary antibodies diluted 1∶100 in blocking buffer. After two rinses with PBS, the sections were incubated in the dark for 1 hour at 37°C with rabbit secondary antibody diluted 1∶500 in normal rabbit serum. Slides were rinsed in PBS before the addition of Topro3 nuclear stain (Invitrogen, Grand Island, NY) and then mounted with Prolong Gold mounting media (Invitrogen). Confocal images were captured using Zeiss LSM 510 Axioskop 2 microscope (Zeiss Microimaging, Thornwood, NY) and analyzed with Zen 2007 software (Zeiss, San Diego, CA).
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5

Confocal Microscopy Analysis of Labeled RBCs

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RBCs were fixed using 0.1% glutaraldehyde, stained with Alexa Fluor 488 phalloidin (5 units/mL), and analyzed by confocal microscopy (Yau et al., 2012 (link)). Confocal laser scanning microscopy analysis was performed with a Duo-Scan system (LSM 5 LIVE; Carl Zeiss Inc., Thornwood, NY) using a 63 × 1.4 NA oil immersion objective. Laser 489 nm line was applied for excitation and emission was collected with 518 nm filter. Images were acquired using ZEN 2007 software (Carl Zeiss, Inc.). Whole cell and biconcave area diameters were determined by drawing a horizontal line through the center of each target RBC and calculating the distances between two points where fluorescent intensities were most different.
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6

Quantifying Platelet Adhesion and Cytoskeleton

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Glass cover slips were coated with fibrinogen overnight at 4°C. Non-specific binding was blocked by incubating cover slips with bovine serum albumin (BSA, 1%) in Tyrode’s-HEPES buffer at 37°C. Cover slips were rinsed with Tyrode’s-HEPES buffer after removing BSA. Aspirin (1mM) treated washed murine platelets containing apyrase (3 U/ml) were layered over cover slips in the presence or absence of Rhosin. After a five minute incubation at 37°C the cover slips were rinsed with PBS to remove free platelets. Platelets on cover slips were then fixed with 4% paraformaldehyde for ten minutes, rinsed with PBS twice and permeabilized with 0.1% Triton X-100 for 60 seconds. After two rinses with PBS platelets were stained with Alexa 594-phalloidin to visualize F-actin [5 (link)]. A Carl Zeiss LSM-510 confocal Axioplan 200 microscope and a Plan-Neofluar 100x/1.45 oil objective was used to generate platelet images. Digital images were processed using Zen 2007 software from Carl Zeiss.
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7

Platelet Adhesion and Spreading on Fibrinogen

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Platelet spreading on fibrinogen was assayed as previously described [4 (link)]. Briefly, glass cover slips were coated with fibrinogen overnight at 4 °C. Non-specific binding was blocked by incubating cover slips with bovine serum albumin (BSA, 1%) in Tyrode’s-HEPES buffer at 37 °C. Cover slips were rinsed with Tyrode’s-HEPES buffer after removing BSA. Aspirin (1 mM)-treated washed human platelets containing apyrase (3 U Ml−1) were layered over cover slips in the presence or absence of Phox-I. After 10 min incubation at 37 °C the cover slips were rinsed with phosphate buffered saline (PBS) to remove free platelets. Platelets on cover slips were then fixed with 4% paraformaldehyde for 10 min, rinsed with PBS twice and permeabilized with 0.1% Triton X-100 for 60 s. After two rinses with PBS, platelets were stained with Alexa 594-phalloidin to visualize F-actin. A Carl Zeiss LSM-510 confocal Axioplan 200 microscope and a Plan-Neofluar 100×/1.45 oil objective were used to generate platelet images. Digital images were processed using Zen 2007 software from Carl Zeiss (Thornwood, NY, USA).
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