Bioimaging Wiki

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<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=zeiss_cell_observer_map_new.png">Room P3-A-10</a> (<img src="/facility/bioimaging/lib/exe/fetch.php?media=phone_neg.png" width=15> 47331) <br> 
<b>Manufacturer</b>: <a href="http://www.zeiss.de/micro" target="_blank">Carl Zeiss MicroImaging</a><br>
<b>Model</b>: Axio Observer<br>
<b>Nickname</b>: "Cell Observer"<br>
<b>Software</b>: ZEN 2 (blue edition)<br>
<b>Year</b>: 2015 <br>
<b>SN</b>: 3851002396<br>
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&rarr; <a href="https://imm.medicina.ulisboa.pt/intranet/booking/125"><img src="/facility/bioimaging/lib/exe/fetch.php?media=date.png">  Zeiss Cell Observer Booking</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=zeiss_cell_observer_quality"><img src="/facility/bioimaging/lib/exe/fetch.php?media=list-icon.png" width=18> Zeiss Cell Observer Quality Control</a>
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&rarr; <a href="/facility/bioimaging/doku.php?id=zeiss_cell_observer_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Zeiss Cell Observer Usage Statistics</a>
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===== Microscope overview =====
The Zeiss Cell Observer is a fully motorized inverted //widefield fluorescence microscope// ideal for live-cell imaging applications. It is equipped with a large cage incubator and a small stage incubator for temperature control and CO2 supply and with Definite Focus for hardware focus control during long time-lapse acquisitions. Using the ZEN 2 software you can control the motorized filters, shutters and stage to simultaneously set up multi-color time-lapse imaging experiments in multiple stage positions. Its sensitive cooled Axiocam 506m camera allows you to capture weak fluorescent signals and minimize photobleaching/photodamage in light sensitive samples. You can also perform Z-stack acquisition and use [[https://huygens.i3s.up.pt/login.php|PPBI Huygens RM]] [[http://micro.magnet.fsu.edu/primer/digitalimaging/deconvolution/deconvolutionhome.html|deconvolution]] server to significantly improve image resolution even in thick samples. If don't want to use deconvolution, check out one of the confocal systems such as the point scanners [[zeiss_lsm_710|Zeiss LSM 710]] and [[zeiss_lsm_880|Zeiss LSM 880]] or spinning disks [[3i_marianas_sdc|3i Marianas SDC]] and [[zeiss_cell_observer_sd|Zeiss Cell Observer SD]]. If your personal computer cannot handle all the data you collected, check out the [[big_guy|Big Guy]] or [[colossus|Colossus]]. If you have FISH or other fixed fluorescence slides try the [[leica_dm5000b|Leica DM5000B]] instead.

  * **Microscope**: [[http://www.zeiss.com/microscopy/en_de/products/light-microscopes/axio-observer-for-biology.html|Zeiss Axio Observer]]
  * **Camera**: [[https://www.zeiss.com/microscopy/int/products/microscope-cameras/axiocam-506-mono.html|Axiocam 506 mono CCD]]

{{:warning.png?25|}} Data files older than **1 month** will be automatically deleted on this system, please copy your data to the iMM server using the desktop link.

===== Booking Rules =====
The Zeiss Cell Observer booking is divided in three daily slots:
|  9:00 to 13:00  |  13:00 to 17:00  |  17:00 to 21:00  |

  - A **user** can book at maximum **2 sessions per week**
  - Each **session must fit inside one of the three daily slots** (i.e. a session booked from 11:00 to 14:00 counts as 2 sessions)
  - The above rules do not apply for **weekends** and for work days **before 9:00** and **after 21:00**
  - The above rules do not apply for sessions booked on the very same day or **24 hours ahead**
  - Exceptions to these rules require **approval from [[joserino@medicina.ulisboa.pt|José Rino]]**.
  - Users must indicate if they will use the incubator in the booking Description field (write down 37C INCUBATOR)

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

==== Filtersets ====

^  Position  ^  Filterset  ^  Reference  ^  Excitation  ^  Emission  ^
|  1  |  HE GFP  |  [[https://www.micro-shop.zeiss.com/?s=23108437692794b&l=en&p=us&f=f&a=v&b=f&id=489038-9901-000&o=|FS38HE]]  |  450-490 nm  |  500-550 nm  |
|  2  |  HE DsRed  |  [[https://www.micro-shop.zeiss.com/?s=23108437692794b&l=en&p=us&f=f&a=v&b=f&id=489043-9901-000&o=|FS43HE]]  |  538-562 nm  |  570-640 nm  |
|  3  |  DAPI  |  [[https://www.micro-shop.zeiss.com/?s=23108437692794b&l=en&p=us&f=f&a=v&b=f&id=488049-9901-000&o=|FS49]]  |  335-383 nm  |  420-470 nm  |
|  4  |  Cy5  |  [[https://www.micro-shop.zeiss.com/?s=23108437692794b&l=en&p=us&f=f&a=v&b=f&id=488050-9901-000&o=|FS50]]  |  625-655 nm  |  665-715 nm  |
|  5  |  none  |  none  |  none  |  none  |
|  6  |  none  |  none  |  none  |  none  |

==== Objectives ====
^  Magnification  ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  10x  |  EC Plan-Neofluar  |  Air  |  0.30  |  5.2  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420340-9901-000/Objective-EC-Plan-Neofluar-10x-0.30-M27|420340-9901-000]]  |
|  20x  |  Plan-Apochromat  |  Air  |  0.80  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420650-9901-000/Objective-Plan-Apochromat-20x-0.8-M27|420650-9901-000]]  |
|  40x  |  EC Plan-NeoFluar  |  Air  |  0.75  |  0.71  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/440350-9903-000/Objective-EC-Plan-Neofluar-40x-0.75|440350-9903-000]]  |
|  63x  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420782-9900-000/Objective-Plan-Apochromat-63x-1.4-Oil-DIC-M27|420782-9900-000]]  |

**Upon request:**
^  Magnification  ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
|  1.25x  |  EC Epiplan-Neofluar  |  Air  |  0.035  |  4  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/422310-9900-000/Objective-EC-Epiplan-Neofluar-1.25x-0.03-M27|422310-9900-000]]  |
|  5x  |  EC Plan-NeoFluar  |  Air  |  0.16  |  18.5  |  [[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  |  EC Plan-Neofluar Ph 2  |  Air  |  0.50  |  2  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/440341-9904-000/Objective-EC-Plan-Neofluar-20x-0.5-Ph2|440341-9904-000]]  |
|  40x  |  Plan-Apochromat Corr  |  Air  |  0.95  |  0.25  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420660-9970-000/Objective-Plan-Apochromat-40x-0.95-Corr-M27|420660-9970-000]]  |
|  40x  |  Plan-Neofluar Ph3  |  Oil  |  1.30  |  0.20  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/440451-9903-000/Objective-EC-Plan-Neofluar-40x-1.30-Oil-Ph3|440451-9903-000]]  |
|  63x  |  Plan-Apochromat Ph3  |  Oil  |  1.4  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420781-9910-000/Objective-Plan-Apochromat-63-1.4-Oil-Ph3-M27|420781-9910-000]]  |
|  100x  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.17  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/440782-9902-000/Objective-Plan-Apochromat-100x-1.40-Oil-DIC|440782-9902-000]]  |

==== Camera ====
^  Model  ^  Type  ^  Frame Size  ^  Pixel Size (µm)  ^
|  [[https://www.zeiss.com/microscopy/int/products/microscope-cameras/axiocam-506-mono.html|Axiocam 506 mono]]  |  CCD  |  2752 x 2208  |  4.54 x 4.54  |
===== System Turn On Procedures =====
  * Turn on the HXP 120 fluorescent light source
{{zeiss_axio_observer_hxp.jpg?120|}}
  * Turn on the temperature and CO2 controller (if you need them).
{{zeiss_axio_observer_temp.jpg?80|}}
  * If you need CO2, open the valve
{{zeiss_axio_observer_co2.jpg?80|}}
  * Turn on the motorized stage controller (**A** on remote control)
{{zeiss_axio_observer_a.jpg?height=150|}}
  * Turn on the Definite Focus controller (if you are going to use it)
{{zeiss_axio_observer_df.jpg?height=150|}}
  * Turn on the microscope power supply (**B** on remote control)
{{zeiss_axio_observer_b.jpg?height=150|}}
  * Turn on the computer
  * Log in to Windows (Biomaging User).
  * Start the **ZEN** software

===== Microscope Turn Off procedures =====
  * Exit the **ZEN 2** software
  * Turn off the computer (not the UPS!)
{{:cell_observer_pc_vs_ups.png?250|}}
  * If you used any __immersion oil in the objectives, clean them up__.
  * Turn off the microscope power supply (B)
  * Turn off the Definite Focus controller (if used)
  * Turn off the Motorized Stage controller (A)
  * Turn off the Temperature and CO2 controller (if used)
  * If there's __another user__ for this microscope in the __next hour__ leave the mercury __lamp power source on, else turn it off__. 
  * Be extra careful in weekends and at the end of the day to make sure that the mercury lamp is not going to be turned on for an excessive time. 

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