Bioimaging Wiki

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<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=zeiss_lsm_980-32_map_2024.png">[Lisbon] Room P2-A-24</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/light-microscopes/confocal-microscopes/lsm-980-with-airyscan-2.html">LSM 980 with Airyscan 2</a><br>
<b>Nickname</b>: "980-32"<br>
<b>Software</b>: ZEN 3.12<br>
<b>Year</b>: 2024 <br>
<b>SN</b>: 2842001157 <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_lsm_980-32_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> Zeiss LSM 980-32 Quality Control</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=zeiss_lsm_980-32_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Zeiss LSM 980-32 Usage Statistics</a>
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===== Microscope overview =====

{{  :confocal_pinhole.png?340}} The Zeiss LSM 980-32 with Airyscan 2 is a [[https://www.youtube.com/watch?v=rTkjQ6Q0p5I|point scanning confocal microscope]] able to generate high-resolution three-dimensional images of thick specimens with high sensitivity, high speed and low photodamage. It is an inverted microscope especially suitable for live cell imaging and photobleaching experiments, equipped with a dark large cage incubator and a stage top incubator for temperature control and CO2 supply, with Definite Focus.3 for hardware focus control during long time-lapse acquisitions, and with an [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research/autoimmersion-module.html|autoimmersion module for water objectives]]. The stage is motorized and furthermore equipped with a piezo for Z displacement so fast 4D imaging is possible in multiple stage positions, using the Tiles Advanced Setup of ZEN blue. It is equipped with [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/ai-sample-finder.html|AI Sample Finder]] for automated sample placement, focus adjustment and identification of the relevant sample areas. Its Airyscan 2 with 32 concentrically arranged GaAsP detection elements is able to collect all light from an Airy pattern simultaneously, allowing for increased resolution (120 nm laterally and 350 nm axially in SR mode, at 488 nm). It can also be used in [[https://www.youtube.com/watch?v=tUiEa7vcggQ|Multiplex Mode]], which enables parallel excitation and detection in 4Y or 8Y modes (speed improvement of 4x/8x maintaining Airyscan sensitivity). Its scanning unit further includes a [[https://imm.medicina.ulisboa.pt/facility/bioimaging/lib/exe/fetch.php?media=32-channel_quasar.png|32-channel GaAsP detector]] for simultaneous [[https://zeiss-campus.magnet.fsu.edu/articles/spectralimaging/introduction.html|spectral imaging and separation of fluorescent labels]] and two PMT detectors. It is equipped with lasers from violet to far red (405, 445, 488, 514, 561, 594 and 639 nm excitation wavelengths). Its[[https://www.zeiss.com/microscopy/en/about-us/newsroom/press-releases/2021/zeiss-lsm-plus-and-zeiss-airyscan-joint-deconvolution.html|LSM Plus deconvolution]] mode enhances signal-to-noise ratio by acting as a denoising step post image acquisition, allowing for high acquisition speed and low laser power. Using its [[https://www.zeiss.com/microscopy/en/about-us/newsroom/press-releases/2021/zeiss-lsm-plus-and-zeiss-airyscan-joint-deconvolution.html|Airyscan Joint Deconvolution (jDCV)]] option, the resolution can be improved to 90 nm (XY) and 270 nm (Z). A dedicated workstation is also available for Direct Processing during acquisition.

  * **Microscope**: [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html|Zeiss Axio Observer]]
  * **LED Illumination**: [[https://www.zeiss.com/microscopy/en/products/accessories/colibri.html|Zeiss Colibri 7]]
  * **Camera (right port)**: [[https://www.zeiss.com/microscopy/en/products/cameras/axiocam-305-mono.html|Axiocam 305m]]
  * **Features**
    * |  [[https://www.imdik.pan.pl/images/Us%C5%82ugi_dokumenty/Przydatne_informacje/2d_Definite_Focus_information.pdf|Definite Focus.3]]
    * | [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research/autoimmersion-module.html|Auto-immersion Module]]
    * | [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/ai-sample-finder.html|AI Sample Finder]]
    * | [[https://www.zeiss.fr/content/dam/Microscopy/fr/download/note_application_a_ten_color.pdf|Spectral Imaging]]
    * | [[https://www.youtube.com/watch?v=tUiEa7vcggQ|Airyscan 2 Multiplex]]
    * | [[https://www.zeiss.com/microscopy/en/about-us/newsroom/press-releases/2021/zeiss-lsm-plus-and-zeiss-airyscan-joint-deconvolution.html|LSM Plus]]
    * | [[https://www.zeiss.com/microscopy/en/about-us/newsroom/press-releases/2021/zeiss-lsm-plus-and-zeiss-airyscan-joint-deconvolution.html|Joint Deconvolution]]

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<p align="center"><iframe width="420" height="236" src="https://www.youtube.com/embed/Ji_PVld77Gs" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe></p>
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  * [[https://www.youtube.com/watch?v=zA4xqq-EL9g|ZEISS Webinar: LSM 980 Airyscan 2 Multiplex mode]]

{{: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.

===== Booking Rules =====
  - **Users** can book at maximum **8 hours per week**
  - This usage restriction does not apply for **weekends** and for working days **before 9:00** and **after 18:00**
  - Exceptions to these rules require **approval from [[joserino@medicina.ulisboa.pt|José Rino]]**.

===== System components =====

==== LASERs ====
^  Laser Unit  ^  Wavelength  ^  Maximum Power  ^
|  405  |  405 nm  |  15 mW  |
|  445  |  445 nm  |  10 mW  |
|  488  |  488 nm  |  13 mW  |
|  514  |  514 nm  |  13 mW  |
|  561  |  561 nm  |  13 mW  |
|  594  |  594 nm  |  4 mW  |
|  639  |  639 nm  |  10 mW  |

==== Objectives ====
^  Magnification   ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  5x  |  EC Plan-NeoFluar  |  Air  |  0.16  |  13.6  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420330-9901-000/Objective-EC-Plan-Neofluar-5x-0.16-M27|420330-9901-000]]  |
|  20x  |  Plan-Apochromat  |  Air  |  0.80  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420650-9903-000/Objective-Plan-Apochromat-20x-0.8-M27|420650-9903-000]]  |
|  40x  |  LD LCI Plan-Apochromat Corr  |  Water  |  1.20  |  0.41  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420862-9970-799/Objective-LD-LCI-Plan-Apochromat-40x-1.2-Imm-Corr-DIC-M27|420862-9970-799]]  |
|  63x  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420782-9900-799/Objective-Plan-Apochromat-63x-1.4-Oil-DIC-M27|420782-9900-799]]  |

==== LEDs (Ocular) ====
^  Line  ^  Wavelength  ^
|  UV  |  385 nm  |
|  B  |  475 nm  |
|  G  |  555 nm  |
|  R  |  630 nm  |

==== Filterset (Ocular) ====

^  Position  ^  Filterset  ^  Reference  ^  Excitation  ^  Dichroic  ^  Emission  ^
|  1  |  QUAD  |  [[https://www.micro-shop.zeiss.com/en/us/shop/filterAssistant/filtersets/489090-9100-000|  FS90HE]]  |  370-400 nm  |  405 nm  |  410-440 nm  |
|  :::  |  :::  |  :::  |  450-488 nm  |  493 nm  |  499-529 nm  |
|  :::  |  :::  |  :::  |  540-570 nm  |  575 nm  |  580-605 nm  |
|  :::  |  :::  |  :::  |  615-648 nm  |  653 nm  |  659-759 nm  |

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

The system should be always on, you only need to:
  * Turn on the computer (if needed)
  * Log into Windows with your Agendo credentials
  * Start **ZEN**

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

If there is another user for this microscope in the __next hour__:
  * Exit the ZEN software, leave the lasers on
  * Log off the computer
  * Clean up immersion objectives (gently wipe with optic cleaning paper and EtOH embedded paper)
Else:
  * Turn off the lasers on **ZEN**
  * Clean up immersion objectives (gently wipe with optic cleaning paper and EtOH embedded paper)
  * Exit the ZEN software
  * Log off the computer

===== Microscope Turn On Procedure (after complete shutdown) =====

If the system is completely off, please follow this procedure:

  * Turn on the ''MAIN SWITCH''
{{::zeiss_lsm_980_main_switch.png?100|}}
  * Turn on the ''COMPONENTS'' switch
{{::zeiss_lsm_980_components.png?100|}}
  * Turn on the Laser key
  * Turn on the computer
  * Log into Windows with your Agendo credentials
  * Start the **ZEN** software

===== Microscope Turn Off Procedure (for complete shutdown) =====

Please only shutdown the system if instructed to do so by the Bioimaging Staff.

  * Turn off the lasers on **ZEN**
  * Exit the ZEN software
  * Shutdown the computer
  * Turn off the Laser key
  * Turn off the ''COMPONENTS'' switch
  * Turn off the ''MAIN SWITCH''

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