Bioimaging Wiki

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<b>Location</b>: [Oeiras] Room 0B02<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/widefield-microscopes/axio-imager-2-for-life-science-research.html">Zeiss Axio Imager 2 with Apotome 2</a><br>
<b>Nickname</b>: Apotome<br>
<b>Software</b>: Zen 3.1<br>
<b>Year</b>:  2019<br>
<b>SN</b>:  <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=imager_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> ZEISS Axio Imager with Apotome 2 Quality Control</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=imager_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  ZEISS Axio Imager with Apotome 2 Usage Statistics</a>
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===== Microscope overview =====

The “Zeiss Imager2 + Apotome2" is a fully automated upright microscope capable of
magnifications from 2.5x to 160x and equipped with two cameras: On the left port a 5MPx CMOS
color camera ([[https://www.zeiss.com/microscopy/en/products/cameras/axiocam-105-color.html|Axiocam 105 RGB]], for brightfield/DIC) and on the top port a high sensitivity 4Mpx
monochrome sCMOS camera ([[https://www.biomedical-instruments-trading.com/products/video-devices/568-hamamatsu-orca-flash-4-0-v2|Hamamatsu Flash 4.0v2]], for fluorescence). The system has a
Colibri7 excitation light source with 5 LEDs (see table below). The system’s stage, which can
accommodate 8 slides simultaneously, is motorized in XYZ, capable of z-stacks, multiple
positions or tile & stitching acquisition (thereby allowing acquisition of large fields of view with
several hundred megapixels!).
The Imager is also equipped with ApoTome.2, which allows optical sectioning of fluorescent
samples using structured illumination. A grid pattern is placed on the illumination path and is
projected and shifted sideways; 3 (or more) images are acquired and between each image the grid
is moved 1/3 of its cycle. This movement generates images where only the in-focus light is
modulated by the grid pattern while out-of-focus light is largely unaffected by the grid. By
subtracting pairs of these images, the system removes out-of-focus light and the grid pattern, thus
creating an optical section of the sample.


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

===== Colibri7 excitation lines (LED) ====

^  Excitation Lines (nm)  ^  Power (mW; @ 10x obj)  ^
|  385  |  ~160*  |
|  475  |  ~120  |
|  555  |  ~20  |
|  590  |  ~14  |
|  630  |  ~44  |

* don't exceed 5% power as this line bleaches samples quickly.

==== Emission Filters ====

^  Filter name  ^  Transmission(nm)  ^  Reference  ^
|  BFP  |  450/40  | [[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  |  425/50  | [[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  |  LP590  | [[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  |  690/50  | [[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  | - |
|  mPlum  |  629/62  | [[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  |  425/514/592/709  | [[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]] |

==== Objectives ====
^  Magnification  ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  2.5x  |  Plan-Neofluar  |  air  |  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  |  Plan-Neofluar  |  air  |  0.3  |  5.5  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420340-9900-000/Objective-EC-Plan-Neofluar-10x-0.30-M27|420340-9900-000]]  | 
|  20x  |  Plan-Apochromat  |  air  |  0.8  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420650-9902-000/Objective-Plan-Apochromat-20x-0.8-M27|420650-9902-000]]  | 
|  40x  |  Plan-Apochromat  |  air  |  0.95  |  0.25  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420660-9970-000/Objective-Plan-Apochromat-40x-0.95-Corr-M27|420660-9970-000]]  | 
|  40x  |  Plan-Neofluar  |  oil  |  1.3  |  0.21  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420462-9900-000/Objective-EC-Plan-Neofluar-40x-1.30-Oil-DIC-M27|420462-9900-000]]  | 
|  100x  |  Plan-Apochromat  |  oil  |  1.4  |  0.17  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420792-9900-000/Objective-Plan-Apochromat-100x-1.40-Oil-DIC-M27|420792-9900-000]]  | 

==== Camera ====

^  Model  ^  Frame Size  ^  Pixel Size (µm)  ^  Quantum Efficiency  ^
|  [[https://www.biomedical-instruments-trading.com/products/video-devices/568-hamamatsu-orca-flash-4-0-v2|Hamamatsu ORCA-Flash4.0 V2]]  |  2048 x 2048  |  13.3 x 13.3  |  70 %  |
===== Microscope Turn On Procedure =====

  * Turn on the ''Power Supply''
{{::oeiras_apotome_turningon1.jpg?300|}}
  * Turn on the ''Microscope Body''
{{::oeiras_apotome_turningon2.jpg?300|}}
  * Turn on the computer
  * Log In into Windows with your Agendo credentials
  * Start the **Zen** software

===== Microscope Turn Off Procedure =====

  * Exit the **Zen** software
  * Log off from the computer
  * Turn off the ''Microscope Body''
  * Turn off the ''Power Supply''

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