Bioimaging Wiki

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<a href="/facility/bioimaging/lib/exe/fetch.php?media=lsm_900.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=lsm_900.jpg" width=300></a>
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<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=bartolomeu_dias_wing_2025_-_zeiss_lsm_900.png">[Oeiras] Room 0B03</a><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-900-with-airyscan-2.html">LSM 900 with Airyscan 2</a><br>
<b>Nickname</b>: "900"<br>
<b>Software</b>: ZEN 3.12<br>
<b>Year</b>:  2022<br>
<b>SN</b>: 2901000180<br>
&nbsp <br>
Data will be deleted after: <b>1 month</b>
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&nbsp <br>
&rarr; <a href="/facility/bioimaging/doku.php?id=oeiras_lsm_900_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> ZEISS LSM 900 with Airyscan 2 Quality Control</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=oeiras_lsm_900_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  ZEISS LSM 900 with Airyscan 2 Usage Statistics</a>
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===== Microscope overview =====

{{  :confocal_pinhole.png?340}} The Zeiss LSM 900 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 and with Definite Focus.3 for hardware focus control during long time-lapse acquisitions. 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. 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 modes. The result is a speed improvement by a factor of 4x, while maintaining the sensitivity of Airyscan. Its scanning unit further includes two PMT detectors as well as a GaAsP detector for increased sensitivity (45% QE compared to ~25% QE for conventional PMT). It is equipped with lasers from violet to far red (405, 488, 561 and 639 nm excitation wavelengths). The [[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. With [[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)]] the resolution can be improved to 90 nm (XY) and 270 nm (Z).

  * **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/odXtaRLHhIQ" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe></p>
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{{: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.


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

==== LASERs ====

^  LASER  ^  Wavelength  ^  Maximum Power  ^
|  violet  |  <fc #a600ff>405 nm</fc>  |  15 mW  |
|  blue  |  <fc #00f7ff>488 nm</fc>  |  13 mW  |
|  yellow-green  |  <fc #c6ff00>561 nm</fc>  |  13 mW  |
|  red  |  <fc #ff2600>640 nm</fc>  |  10 mW  |

==== LEDs (for eyepieces) ====

^  Line  ^  Wavelength  ^
|  UV  |  <fc #be00cc>385 nm</fc>  |
|  B  |  <fc #00c0ff>475 nm</fc>  |
|  G  |  <fc #b3ff00>555 nm</fc>  |
|  R  |  <fc #ff4f00>630 nm</fc>  |

==== Objectives ====

^  Magnification   ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  <fc #df2b37>5x</fc>  |  EC Plan-Neofluar  |  Air  |  0.16  |  18.5  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420330-9901-000/Objective-EC-Plan-Neofluar-5x-0.16-M27|420330-9901-000]]  |
|  <fc #fef042>10x</fc>  |  Plan-Apochromat  |  Air  |  0.45  |  2  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420640-9900-000/Objective-Plan-Apochromat-10x-0.45-M27|420640-9900-000]]  |
|  <fc #0aa05c>20x</fc>  |  Plan-Apochromat  |  Air  |  0.80  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420650-9903-000/Objective-Plan-Apochromat-20x-0.8-M27|420650-9903-000]]  |
|  <fc #01b3f5>40x</fc>  |  LD LCI Plan-Apochromat  |  W, Sil, G  |  1.2  |  0.41  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420862-9970-799/Objective-LD-LCI-Plan-Apochromat-40x-1.2-Imm-Corr-DIC-M27|420862-9970-799]]  |
|  <fc #2c80c0>63x</fc>  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420782-9900-799/Objective-Plan-Apochromat-63x-1.4-Oil-DIC-M27|420782-9900-799]]  |


==== Emission Filters ====

^  Filter name  ^  Transmission  ^  Reference  ^
|  BFP  |  <fc #0046ff>450/40 nm</fc>  |  [[https://www.fpbase.org/spectra/?s=2666,2668,2667,2055&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|96 HE]]  |
|  GFP  |  <fc #4aff00>525/50 nm</fc>  |  [[https://www.fpbase.org/spectra/?s=1484,1495,1485,2057&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|38 HE]]  |
|  Alexa 546  |  <fc #ffdf00>LP590 nm</fc>  |  [[https://www.fpbase.org/spectra/?s=1530,1533,1536,2059&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|15]]  |
|  Cy5  |  <fc #ff0000>690/50 nm</fc>  |  [[https://www.fpbase.org/spectra/?s=1547,1550,1543,2068&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|50]]  |
|  DIC  |  < 800 nm  |  -  |
|  mPlum  |  <fc #ff5300>629/62 nm</fc>  |  [[https://www.fpbase.org/spectra/?s=2620,2618,2619,2069&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|64 HE]]  |
|  Quad  |  <fc #5400ff>425</fc>/<fc #1aff00>514</fc>/<fc #ffd900>592</fc>/<fc #ef0000>709</fc> nm  |  [[https://www.fpbase.org/spectra/?s=2657,2601,2602,2658,2577&showY=0&showX=1&showGrid=0&areaFill=1&logScale=0&scaleEC=0&scaleQY=0&shareTooltip=1&palette=wavelength|90 HE]]  |

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

If you are the **first user** of the day:

  * Turn off the power bar
{{::Oeiras_LSM900_powerbar.png?200|}}
  * Turn off Components
  * Turn off Systems
  * Turn on the computer
  * Turn on Systems
  * Turn on Components
  * Turn on the power bar
  * Turn on the incubation module (if needed - turn on 30 mins before acquiring)
{{::Oeiras_LSM900_incubation.png?200|}}
  * Log into Windows with your Agendo credentials
  * Start **ZEN**
Else:
  * Log into Windows with your Agendo credentials
  * Start **ZEN**

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

If there is another user:
  * Clean up immersion objectives 
  * Exit the ZEN software 
  * Log off the computer 
  * Turn off incubation module (if used) 
If you are the **last user** of the day: 
  * Clean up immersion objectives 
  * Exit the ZEN software 
  * Turn off the computer 
  * Turn off incubation module (if used) 

----

[[resources|Back to the Equipment page]]
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