GIMM Bioimaging Wiki

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
<html>
<img src="/facility/bioimaging/lib/exe/fetch.php?media=oeiras_agilent_cytation_5_name_gimm_2024.png">
<table style="border:0px solid white;">
<tr style="border:0px solid white;">
<td style="border:0px solid white;">
<a href="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg" width=300></a>
<td style="border:0px solid white;"> <p style="line-height:1.8">
<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=bartolomeu_dias_wing_2025_-_cytation_5.png">[Oeiras] Room 0B16</a><br> 
<b>Manufacturer</b>:  <a href="https://www.agilent.com/" target="_blank">Agilent</a> <br>
<b>Model</b>:  <a href="https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-multimode-readers/biotek-cytation-5-cell-imaging-multimode-reader-1623202" target="_blank">BioTek Cytation 5 Cell Imaging Multimode Reader</a> <br>
<b>Nickname</b>: Cytation 5 <br> 
<b>Software</b>: Gen 5 Image Prime <br>
<b>Year</b>: 2024 <br>
<b>SN</b>: 2302240B<br>
&nbsp <br>
Data will be deleted after: <b>1 month</b>
&nbsp <br>
&nbsp <br>
&rarr; <a href="/facility/bioimaging/doku.php?id=cytation_5_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> Agilent Cytation 5 Quality Control</a>
 <br> 
&rarr; <a href="/facility/bioimaging/doku.php?id=cytation_5_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Agilent Cytation 5 Usage Statistics</a>
</p>
</td>
</tr>
</table>
</html>

===== Microscope overview =====

The Cytation 5 Cell Imaging Multimode Reader is a fully automated plate and slide reader equipped with an inverted widefield configuration.

This unit is capable of imaging from 4-40x with fluorescence and/or brightfield (mono or RGB). It is equipped with three different excitation LEDs and filter sets (there is a fourth slot which is mainly used for hardware-based autofocus, but which can be replaced by a 4th fluorescence channel upon request).

It is also equipped with an atmosphere control unit for regulating CO2 concentration (for live cell imaging), and capable of setting up for hypoxia conditions also. The multimode detection modules include filter- and monochromator-based fluorescence detection, luminescence, and UV-Vis absorbance detection.

===== System Components =====

==== LEDs ====

^  Line  ^  Wavelength  ^  Reference  ^
|  UV  |  <fc #be00cc>385 nm</fc>  |  1225007  |
|  B  |  <fc #0092ff>465 nm</fc>  |  1225001  |
|  G  |  <fc #42ff00>523 nm</fc>  |  1225003  |
|  Y  |  <fc #ffdf00>590 nm</fc>  |  1225002  |
|  R  |  <fc #ff6b00>623 nm</fc>  |  1225005  |

==== Filtersets available ====

^  Position  ^  Filterset  ^  Excitation  ^  Dichroic  ^  Emission  ^  Reference  ^
|  1  |  LASER Autofocus  |  -  |  -  |  -  |  [[https://www.agilent.com/store/productDetail.jsp?catalogId=1225010&catId=SubCat2ECS_2041516|1225010]]  |
|  2  |  DAPI  |  352-402 nm  |  409 nm  |  <fc #0035ff>417-477 nm</fc>  |  [[https://www.agilent.com/store/en_US/Prod-1225100/1225100|1225100]]  |
|  -  |  GFP  |  453-488 nm  |  497 nm  |  <fc #4aff00>505-545 nm</fc>  |[[https://www.agilent.com/store/en_US/Prod-1225101/1225101|1225101]]  |
|  3  |  Propidium Iodide  |  511-551 nm  |  605  nm  |  <fc #ff0000>619-676 nm</fc>  |[[https://www.agilent.com/store/en_US/Prod-1225111/1225111|1225111]]  |
|  -  |  Texas Red  |  579-594 nm  |  605 nm  |  <fc #ff0000>619-676 nm</fc>  |  [[https://www.agilent.com/store/en_US/Prod-1225102/1225102|1225102]]  |
|  4  |  Cy5  |  608-648 nm  |  660 nm  |  <fc #ff0000>665-705 nm</fc>  |  [[https://www.agilent.com/store/en_US/Prod-1225105/|1225105]]  |

==== Objectives ====

^  Magnification  ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  4x  |  Plan-Semiapochromat Fluorescence  |  Air  |  0.13  |  17  |  [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706528|UPLFLN4X]]  |
|  20x  |  Plan-Semiapochromat Fluorescence  |  Air  |  0.45  |  6.60-7.80  |  [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706550|LUCPLFLN20X]]  |
|  40x  |  Plan-Semiapochromat Fluorescence  |  Air  |  0.6  |  2.70-4.00  |  [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706551|LUCPLFLN40X]]  |

==== Camera ====

^  Model  ^  Frame Size  ^  Pixel Size (µm)  ^  Quantum Efficiency  ^
|  [[https://www.teledynevisionsolutions.com/products/chameleon3-usb3/?model=CM3-U3-50S5M-CS&vertical=machine%20vision&segment=iis|FLIR Chameleon3 CM3-U3-50S5M (mono)]]  |  2448 × 2048  |  3.45 x 3.45  |  69% (at 525 nm)  |

==== Pixel Size ====

Images coming from the Cytation 5 are not calibrated, even though the system has that information available. In the images' metadata you can find the PixelWidth and the ImageWidthMicrons, and by dividing the latter for the first, you get the Pixel Size to calibrate your images.
You can find this information below, per objective and Field Of View (FOV):

^  Objective  ^  FOV  ^  Image Size (pixels)  ^  Image Size (microns)  ^  Pixel Size (microns)  ^
|  4x  |  Full  |  1992 x 1992  |  3474 x 3474  |  ~1.7440 x ~1.7440  |
|  4x  |  75%  |  1496 x 1496  |  2609 x 2609  |  ~1.7440 x ~1.7440  |
|  4x  |  Standard  |  1224 x 904  |  2135 x 1576  |  ~1.7443 x ~1.7434  |
|  20x  |  Full  |  1992 x 1992  |  694 x 694  |  ~0.3484 x ~0.3484  |
|  20x  |  75%  |  1496 x 1496  |  521 x 521  |  ~0.3483 x ~0.3483  |
|  20x  |  Standard  |  1224 x 904  |  427 x 315  |  ~0.3489 x ~0.3485  |
|  40x  |  Full  |  1992 x 1992  |  347 x 347  |  ~0.1742 x ~0.1742  |
|  40x  |  75%  |  1496 x 1496  |  260 x 260  |  ~0.1738 x ~0.1738  |
|  40x  |  Standard  |  1224 x 904  |  213 x 157  |  ~0.1740 x ~0.1737  |

===== CO2 and/or O2 Control Procedure  =====

  * **If you require CO2 and/or O2 control**, turn the **atmosphere controller ON**.
{{cytation_gas_1.png?200|}}
  * Confirm the **CO2 and/or O2 switch is ON**, and set to the desired percentage.
{{cytation_gas_2.png?600|}}
  * **Open the CO2 and/or N2 tap** on the wall.
{{cytation_gas_3.png?200|}}

===== Microscope Turn On Procedure =====

  * Turn on the microscope using the **switch** at the **front of the system**.
{{cytation_turnon_1.png?200|}}
  * Turn the **computer** on (if needed).
{{cytation_turnon_2.png?200|}}
  * **Login** to Windows with your **GIMM Agendo credentials**.

  * Wait for the **button light** in the front to **turn green** (the system will pop out the plate drawer as well).
{{cytation_turnon_3.png?200|}}
  * Open the **Gen 5** software.

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

  * Turn off the microscope using the **switch** at the **front of the system**.
{{cytation_turnon_1.png?200|}}
  * **Log off** the computer.

  * **If you used the gas controller** 
    * Turn gas controller OFF
{{cytation_gas_1.png?200|}}
    * Close all wall taps.
{{cytation_gas_3.png?200|}}

----
[[resources|Back to the Equipment page]]
GIMM Bioimaging Wiki

User Tools

Site Tools

Page Tools
