Bioimaging Wiki

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<a href="/facility/bioimaging/lib/exe/fetch.php?media=lsm_980.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=lsm_980.jpg" width=300></a>
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<b>Location</b>: [Oeiras] Room 0B06<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"<br>

<b>Software</b>: ZEN 3.12 <br>
<b>Year</b>: 2019<br>
<b>SN</b>: 2871000107<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=oeiras_lsm_980_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> ZEISS LSM 980 with Airyscan 2 Quality Control</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=oeiras_lsm_980_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  ZEISS LSM 980 with Airyscan 2 Usage Statistics</a>
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===== Microscope overview =====

{{  :confocal_pinhole.png?340}} The Zeiss LSM 980 with Airyscan 2 is a [[https://www.youtube.com/watch?v=rTkjQ6Q0p5I|point scanning confocal microscope]] is an inverted microscope equipped with a laser scanning head with a total of 6 PMT/GaAsp + 1 Airyscan detectors. The Airyscan can achieve non-diffraction limited optical sectioning with resolutions down to 140nm laterally and ~400nm axially. It also allows acquisition in “Multiplexing” mode(s), which accelerate the acquisition speed (4/8x faster) or in sensitivity mode that enhances the signal-to-noise acquisition.

The microscope is also equipped with a dark heating and atmospheric control chamber to allow live imaging of mammalian cells (O2 control is also possible, upon request). We have available an objective inverter for some intra-vital or open-dish applications (upon request only, requires preparation). 

  * **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]]
  * **Features**
    * |  [[https://www.imdik.pan.pl/images/Us%C5%82ugi_dokumenty/Przydatne_informacje/2d_Definite_Focus_information.pdf|Definite Focus.3]]
    * | [[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 21:00**
  - Exceptions to these rules require **approval from [[joserino@medicina.ulisboa.pt|José Rino]]**.

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

==== Lasers =====

^  Laser  ^  Excitation line  ^  Maximum Power  ^  Description (use)  ^   
|  <fc #ff00ff>405 nm (violet)</fc>  |  405 nm  |  15 mW  |  <fc #00ffff>DAPI, Hoechst</fc>   |  
|  <fc #6495ed>488 nm (blue)</fc>  |  488 nm  |  13 mW  |  <fc #00ff00>GFP, FITC, Alexa488</fc>   |  
|  <fc #00ff00>561 nm (green)</fc>  |  561 nm  |  13 mW  |  <fc #ffa500>RFP, TRITC, Cy3, Dylight Orange</fc>   |  
|  <fc #ff0000>639 nm (red)</fc>  |  639 nm  |  10 mW  |  <fc #cd5c5c>Cy5, APC, Alexa/ATTO633-647</fc>   |  

If you require more laser lines (e.g., 445nm - CFP/Cerulean, 514nm - YFP, or 594nm mCherry/AF594), we suggest as an alternative the [[https://imm.medicina.ulisboa.pt/facility/bioimaging/doku.php?id=zeiss_lsm_980-32|ZEISS LSM 980-32]] in Lisbon.



==== Objectives ====
^  Magnification   ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  2.5x  |    |  -  |  0.085  |  8.8  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420320-9902-000/Objective-EC-Plan-Neofluar-2.5x-0.085-M27|420320-9902-000]]  |
|  10x  |  EC Plan-Neofluar  |  Air  |  0.45  |  2.0  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420640-9900-000/Objective-Plan-Apochromat-10x-0.45-M27|420640-9900-000]]  |
|  20x  |  Plan-Apochromat  |  Air  |  0.75  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420150-9900-000/Objective-Fluar-20x-0.75-M27|420150-9900-000]]  |
|  25x  |    |  W/Sil/Gly/Oil*  |  0.80  |  0.57  |   [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420852-9870-790/Objective-LD-LCI-Plan-Apochromat-25x-0.8-Imm-autocorr-DIC-M27|420852-9870-790]]  |  
|  40x  |  LD C-Apochromat Corr  |  Water  |  1.10  |  0.62  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/421867-9970-000/Objective-LD-C-Apochromat-40x-1.1-W-Corr-M27|421867-9970-000]] |  
|  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]]  |

*ask staff for help setting up the proper immersion medium setting


==== Detector(s) ====

1x blue-green multialkali PMT (15-20% QE)

4x GaAsP PMT spectral detectors (tunable between 450-750 nm) (~45% QE)

1x green-red multialkali PMT  (10-25% QE)

1x T-PMT detector (brighfield)

1x Airyscan2 detector (~45% QE after processing Airyscan data)

==== Airyscan2 emission filters =====
^  Position  ^  Emission  ^
|  1  |  Plate  |
|  2  |  BP 420 - 480 + BP 495 - 550  |
|  3  |  BP 420 - 470 + BP 570 - 630  |
|  4  |  BP 420 - 500 + LP 605  |
|  5  |  BP 465 - 505 + BP 525 - 585  |
|  6  |  BP 495 - 550 + BP 570 - 630  |
|  7  |  BP 495 - 555 + LP 660  |
|  8  |  BP 570 - 620 + LP 660  |


==== Eyepiece filterset(s) (COLIBRI LED illumination) =====
^  Position  ^  Transmission  ^  Description (use)  ^  Excitation   ^
|  DAPI  |  445/50 nm  |  <fc #00ffff>DAPI, CFP or Hoechst filter</fc>  |  385nm   |
|  GFP   |  525/50 nm  |  <fc #00ff00>RFP or TRITC (LongPass)</fc>  |   493nm  |
|  RFP   |  LP590 nm  |  <fc #ffa500>GFP or FITC filter</fc>  |  555nm  |
|  Mirror   |  -  |  Mirror for LSM  |  -  |  


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

The system should be always on, you only need to:
  * Turn on HXP (if needed)
  * 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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