GIMM Bioimaging Wiki

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<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=zeiss_cd7_map_2024.png">[Lisbon] Room P0-A-30</a> (<img src="/facility/bioimaging/lib/exe/fetch.php?media=phone_neg.png" width=15> 47219) <br> 
<b>Manufacturer</b>: <a href="http://www.zeiss.de/micro" target="_blank">ZEISS Microscopy</a><br>
<b>Model</b>: <a href="https://www.zeiss.com/microscopy/en/products/imaging-systems/celldiscoverer-7.html">Celldiscoverer 7 with LSM 900</a><br>
<b>Nickname</b>: "CD7"<br>
<b>Software</b>: ZEN 3.13 (ZEN celldiscoverer)<br>
<b>Year</b>: 2022 <br>
<b>SN</b>: 4648000055<br>
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Data will be deleted after: <b>1 month</b>
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&rarr; <a href="/facility/bioimaging/doku.php?id=zeiss_cd7_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Usage Statistics</a>
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===== Microscope overview =====

{{  :confocal_pinhole.png?340}} The Zeiss Celldiscoverer 7 is a fully integrated and motorized high-end inverted widefield and [[https://www.youtube.com/watch?v=rTkjQ6Q0p5I|point scanning confocal]] fluorescence imaging system ideal for automated live-cell imaging in multi-well plates and Petri dishes. It offers a fully integrated incubation system with temperature and CO2 control and [[https://www.imdik.pan.pl/images/Us%C5%82ugi_dokumenty/Przydatne_informacje/2d_Definite_Focus_information.pdf|Definite Focus.3]] for hardware focus control. The ZEN software can automatically calibrate the system and adapt it to your sample by recognizing different sample carriers, determining their bottom thickness and material and adjusting the objectives correction ring to compensate for spherical aberrations. You can use Petri dishes, chamber slides, multi-well plates, plastic or glass, thin or thick vessel bottoms, low-skirt or high-skirt plates. When using the 50x water immersion objective, automated immersion supply and removal is available for time lapse experiments over several days or extensive scanning processes on multi-well plates. In widefield mode, the fluorescence excitation unit combines seven LEDs – from deep blue to far-red - for high-speed multi-channel imaging and its sensitive cooled Axiocam 712 camera allows you to capture weak fluorescent signals and minimize photobleaching/photodamage in light sensitive samples. In confocal mode, the LSM 900 with Airyscan 2 allows for 3D imaging with increased resolution (120 nm laterally and 350 nm axially in SR mode, at 488 nm) and photomanipulation for FRAP, FRET and related techniques. It can also be used in [[https://www.youtube.com/watch?v=tUiEa7vcggQ|Multiplex Mode]], which enables parallel excitation and detection in 2Y mode (speed improvement of 2x maintaining Airyscan sensitivity).

  * **LED Illumination**: [[https://www.zeiss.com/microscopy/en/products/accessories/colibri.html|Zeiss Colibri 7]]
  * **Camera**: [[https://www.zeiss.com/microscopy/en/products/cameras/axiocam-712-mono.html|Axiocam 712 mono CMOS]]
  * **Confocal Scanning Head**: [[https://www.zeiss.com/microscopy/en/products/light-microscopes/confocal-microscopes/lsm-900-with-airyscan-2.html|LSM 900 with Airyscan 2]]

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<iframe width="420" height="236" src="https://www.youtube.com/embed/ASj3VPzc7OA?si=PvU0VrWtCqSbcbXz" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe> <iframe width="420" height="236" src="https://www.youtube.com/embed/odXtaRLHhIQ?si=66AeWpxof84PRBsu" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe></p>
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  * [[https://www.zeiss.com/microscopy/en/resources/insights-hub/life-sciences/the-smart-microscope-for-automated-workflows-celldiscoverer-7-with-lsm-900.html|ZEISS Webinar: The Smart Microscope for Automated Workflows - Celldiscoverer 7 with LSM 900]]


{{:warning.png?25|}} Data files older than **1 month** will be automatically deleted on this system, please copy your data to the GIMM server using the desktop link.

===== Robotic Loader Integration =====

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            <iframe width="225" height="400" src="https://www.youtube.com/embed/72Hi3Ug6_0k?si=Wc__G1wHNSd8PQBd" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
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       The ZEISS Celldiscoverer 7 integrates with an <b>advanced robotic loader</b>, <b>automated liquid handler</b>, and <b>incubator</b> to enable high-throughput, fully automated workflows for live-cell imaging. This integration allows for automated plate loading, liquid handling, and imaging of multiple plates stored under controlled conditions in the incubator, reducing manual intervention and simplifying complex experimental protocols. The loader supports <a href="https://theautomatedlab.com/article.html?content=microplates#:~:text=Standardization:%20The%20SBS%20Footprint,on%20a%20predictable%20plate%20footprint">all SBS multi-well plate formats</a>. The liquid handler includes a custom HEPA downflow to prevent contamination during sample preparation for cell-based screening assays.<br>
           <br>
           • Robotic loader: <a href="https://paa-automation.com/product/kx2-500/">Peak Analysis & Automation KX2-500</a><br>
           • Automated incubator: <a href="https://www.thermofisher.com/order/catalog/product/51032950">Thermo Fisher Cytomat 2 C</a><br>
           • Automated Liquid Handler: <a href="https://www.agilent.com/en/product/automated-liquid-handling/automated-liquid-handling-platforms/bravo-automated-liquid-handling-platform">Agilent Bravo</a><br>
           <br>
           <a href="https://paa-automation.com/product/kx2-500/"><img src="/facility/bioimaging/lib/exe/fetch.php?media=kx_2-500.png" width=118></a><a href="https://www.thermofisher.com/order/catalog/product/51032950"><img src="/facility/bioimaging/lib/exe/fetch.php?media=cytomat.png" width=137></a><a href="https://www.agilent.com/en/product/automated-liquid-handling/automated-liquid-handling-platforms/bravo-automated-liquid-handling-platform"><img src="/facility/bioimaging/lib/exe/fetch.php?media=bravo.png" width=137></a>
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===== System components =====

==== LASERs (confocal) ====

^  LASER  ^  Wavelength  ^  Maximum Power  ^
|  Violet  |  <fc #a600ff>405 nm</fc>  |  5 mW  |
|  Blue  |  <fc #00f7ff>488 nm</fc>  |  10 mW  |
|  Yellow-Green  |  <fc #c6ff00>561 nm</fc>  |  10 mW  |
|  Red  |  <fc #ff2100>640 nm</fc>  |  5 mW  |

==== LEDs (widefield) ====
^  Line  ^  Wavelength  ^
|  UV  |  <fc #be00cc>385 nm</fc>  |
|  V  |  <fc #6a00ff>420 nm</fc>  |
|  B  |  <fc #00a9ff>470 nm</fc>  |
|  C  |  <fc #36ff00>520 nm</fc>  |
|  G  |  <fc #d8ff00>567 nm</fc>  |
|  Y  |  <fc #ffdf00>590 nm</fc>  |
|  R  |  <fc #ff6300>625 nm</fc>  |

==== Filtersets (widefield) ====

^  Position  ^  Filterset  ^  Dichroic  ^  Emission  ^  Reference  ^
|  1  |  RQBS  |  405 nm  |  <fc #5400ff>410-440 nm</fc>  |  [[https://www.micro-shop.zeiss.com/en/us/fluorescenceAssistant/filtersets/489090-9110-000|FS90HE]]  |
|  :::  |  :::  |  493 nm  |  <fc #1fff00>499-529 nm</fc>  |  :::  |
|  :::  |  :::  |  575 nm  |  <fc #ffd900>580-605 nm</fc>  |  :::  |
|  :::  |  :::  |  653 nm  |  <fc #ef0000>659-759 nm</fc>  |  :::  |
|  2  |  RTBS  |  450 nm  |  <fc #009cff>455-479 nm</fc>  |  [[https://www.micro-shop.zeiss.com/en/us/fluorescenceAssistant/filtersets/489091-9110-000|FS91HE]]  |
|  :::  |  :::  |  538 nm  |  <fc #b3ff00>543-568 nm</fc>  |  :::  |
|  :::  |  :::  |  610 nm  |  <fc #ff0000>615-760 nm</fc>  |  :::  |
|  3  |  RTBS  |  405 nm  |  <fc #5400ff>410-440 nm</fc>  |  [[https://www.micro-shop.zeiss.com/en/us/fluorescenceAssistant/filtersets/489092-9110-000|FS92HE]]  |
|  :::  |  :::  |  493 nm  |  <fc #46ff00>499-549 nm</fc>  |  :::  |
|  :::  |  :::  |  610 nm  |  <fc #ff0000>616-761 nm</fc>  |  :::  |
|  4  |  RDBS  |  493 nm  |  <fc #1fff00>498-530 nm</fc>  |  FS93HE  |
|  :::  |  :::  |  575 nm  |  <fc #ffad00>580-630 nm</fc>  |  :::  |

==== Objectives ====
^  Model  ^  Immersion  ^  WD (mm)  ^  NA  ^   Magnification changer  ^  Magnification  ^
|  <fc #ed0707>Plan-Apochromat 5x / 0.35</fc>  |  Air  |  5.10  |  0.12  |  0.5x   |  2.5x  |
|  :::  |  :::  |  :::  |  0.25  |  1x  |  5x  |
|  :::  |  :::  |  :::  |  0.35  |  2x  |  10x  |
|  <fc #f9fb1a>Plan-Apochromat 20x / 0.7</fc>  |  Air  |  2.20  |  0.35  |  0.5x   |  10x  |
|  :::  |  :::  |  :::  |  0.70  |  1x  |  20x  |
|  :::  |  :::  |  :::  |  :::  |  2x  |  40x  |
|  <fc #32cb35>Plan-Apochromat 20x / 0.95</fc>  |  Air  |  0.76  |  0.50  |  0.5x   |  10x  |
|  :::  |  :::  |  :::  |  0.80  |  1x  |  20x  |
|  :::  |  :::  |  :::  |  0.95  |  2x  |  40x  |
|  <fc #2190fd>Plan-Apochromat 50x / 1.2 W</fc>  |  Water  |  0.84  |  1.20  |  0.5x   |  25x  |
|  :::  |  :::  |  :::  |  :::  |  1x  |  50x  |
|  :::  |  :::  |  :::  |  :::  |  2x  |  100x  |

==== Camera (widefield) ====
^  Model  ^  Type  ^  Frame Size  ^  Pixel Size (µm)  ^
|  [[https://www.zeiss.com/microscopy/en/products/cameras/axiocam-712-mono.html|Axiocam 712 mono CMOS]]  |  CMOS  |  4096 x 3008  |  3.45 x 3.45  |

===== How to start your session =====

If you are the **first user** of the day:
  * Turn off the Main Switch (bottom right of the CD7)
{{::cd7_main_switch.png?250|}}
  * Turn on the computer
  * Turn on Main Switch
  * Activate the CD7 by pressing the "Standby" button (to the left of the touch panel)
{{::cd7_standby.png?250|}}
  * Log into Windows with your Agendo credentials
  * Start **ZEN**
  * Open the **Main valve** of the CO2 tank (if needed) - do not change the pressure settings!
{{::cd7_co2.png?130|}}

Else:
  * Log into Windows with your Agendo credentials
  * Start **ZEN**
  * Open the **Main valve** of the CO2 tank (if needed) - do not change the pressure settings!

===== How to end your session =====

If there is another user:
  * Exit the ZEN software
  * Log off the computer
If you are the **last user** of the day:
  * Close the main valve of the CO2 tank (if used)
  * Turn off the lasers on **ZEN**
  * Exit the ZEN software
  * Turn off the computer
  * Press the "Standby" button (to the left of the touch panel).

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