Cell Discoverer 7 (CD7)

Frequently Asked Questions:

  • How do I save and access my data?

Save the data in:

→ open the driver data (D :) “Data_Bioimg”

→ open folder with your Weizmann user name

→ open a new folder with the date (crucial)

→ save the data (characters like ~!@#$%^&*()`;’:<>,/?[]{}  are not allowed, and files including them are not copied)

Once you are done, the computer will synchronize the correctly saved data to the “bioimg” server.

To see the data on your PC, follow the instructions in this link: BioImg Storage Server system.

**When starting to work with the Bioimaging system for the first time, please make sure you have a UNIX ID added to your WIS ID (you can check it with your unit administrator)
  • How do I stitch my tile data?

Go to:

Processing → Method: “stitching” → settings: “1*” → click “New Output” →

Check “Fuse Tiles” + “Correct shading.”

  • How do I split sense?

Go to:

Processing → Method: “split sense.”

  • How can I visualize the data on my pc?

Download ZEN LITE

Or you can work on “Maui” or “Capri”, read more on our Image Analysis Software and Workstations.

How do I start?

  1. Turn OFF the computer.

  2. Turn ON the microscope

  3. Wait until the microscope is fully loaded

  4. Turn ON the computer

  5. Enter ZEN software

  6. Turn on incubation if needed (put the pump level on “5”)

  7. “SAMPLE” tab:

    1. chose the correct sample carrier (blue arrow)

    2. Clean the plate bottom with Ethanol. Make sure the plate is not cracked and is free from debris.

  8. Place the sample in the sample carrier and place it in the tray. **make sure you put it in the right orientation A1”.

  9. Click “LOAD SAMPLE”

  10. Once the loading is done, a “CarrierOverview” image and a “Navigation” tab will be created on the Acquisition tab.

  11. “ACQUISITION” tab: go to “smart setup”

  12. Chose camera “selected detector”

    1. Axiocam 506: CMOS, 2.3 MP: 1920 (H) x 1216 (V), pixel size 5.86 μm x 5.86 μm. Fast, more sensitive for weak signals but noisier with lower resolution.

    2. Axiocam 702: CCD, 6 Megapixel: 2752 (H) × 2208 (V), pixel size 4.54 μm x 4.54 μm. Low noise, high-quality image but slow.

  13. Chose channels by clicking “+” and “Add” at the end

  14. Set intensity and exposure time values per each channel: 10% and 100 ms exposure time is a good start

  15. Start visualizing by clicking “LIVE.”

  16. Focus (hold Ctrl and scroll) at low magnification and then go to higher magnifications if needed.

  17. Build your experiament:

    1. Add Z-Stack

    2. Add Tiles

    3. Add Time Series

    4. Use the right Focus Strategy

How to turn OFF the microscope?

  1. Save the data in data (D :) “Data_Bioimg.”

    → open folder with your Weizmann user name

    → open a new folder with the date

    → save the data

  2. Go to the “Sample” tab and click “Eject Tray.”

  3. Take the sample and the insert (if you used one) out.

  4. Put the insert in its place.

  5. Discard the sample.

  6. Turn OFF incubation (temperature, CO2, and pump level)

  7. Exit the software (leave the computer on for the data will synchronize)

  8. Turn OFF the microscope

  9. Leve the area Clean


Fully integrated high-end automated live cell imaging system that enables high sensitivity and focuses stability in live-cell experiments (imaging period: days)

  1. Allows automated recognition of single plate/multi-well plates and chamber slide`s parameters: material (glass/plastic),  thickness, skirt height (for maximal high-res lateral view)

    • Objectives:
      *effective (optical) zoom 0.5X-1X-2X

      • 5x / 0.35  (Working distance 5.10 mm)

      • 20x / 0.7 Autocorr Objective (Working distance 2.20 mm)

      • 20x / 0.95 Autocorr Objective (Working distance 0.76 mm)

      • 50x / 1.2 W Autocorr and Autoimmersion Objective (Working distance 0.84 mm)
        *Automated water injection/removal allows smooth shift between magnifications during experiments

    • Combination of hardware and software-based focus strategies allow fast focus determination and stability over long periods

    • Excitation LEDs : 385, 420, 470, 511, 567, 590, 625. The system is equipped with high-efficiency multiband pass filter sets. Other contrast options include: bright field, DIC, and phase gradient

    • Two cameras: Zeiss Axiocam 506 mono and s CMOS 702

    • Environmental control: temperature range within sample chamber: 30 – 45 °C or cooling unit controls the temperature of the top plate of sample chamber with a temperature range of 14 – 28 °C.

    • An O2-control device for Hypoxia experiments, done by displacement with N2 within the sample chamber.

    • Possibility for smart experimental design: Use Python scripts to customize and automate your workflows.

  • Integrate external image analysis applications into your workflows.

  • Exchange image data with external programs like ImageJ, Fiji, MATLAB, KNIME, or Python.

  • Use feedback for smart experiments.

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