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zeiss_cell_observer [2020/07/09 03:41]
bioimaging
zeiss_cell_observer [2024/01/31 10:55] (current)
bioimaging
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-<a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_wiki_new.png"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_wiki_new.png" width=300></​a>​+<a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_wiki_2022.png"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_wiki_2022.png" width=300></​a>​
 <td style="​border:​0px solid white;">​ <p style="​line-height:​1.8">​ <td style="​border:​0px solid white;">​ <p style="​line-height:​1.8">​
-<​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>​Location</​b>:​ <a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_map_new_p2a24.png">​Room ​P2-A-24</a> (<img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=phone_neg.png"​ width=15> ​47219) <br>  
-<​b>​Manufacturer</​b>:​ <a href="​http://​www.zeiss.de/​micro"​ target="​_blank">​Carl Zeiss MicroImaging</​a><​br>​+<​b>​Manufacturer</​b>:​ <a href="​http://​www.zeiss.de/​micro"​ target="​_blank">​ZEISS Microscopy</​a><​br>​
 <​b>​Model</​b>:​ Axio Observer<​br>​ <​b>​Model</​b>:​ Axio Observer<​br>​
 <​b>​Nickname</​b>:​ "Cell Observer"<​br>​ <​b>​Nickname</​b>:​ "Cell Observer"<​br>​
-<​b>​Software</​b>:​ ZEN (blue edition)<​br>​+<​b>​Software</​b>:​ ZEN 3.0 (blue edition)<​br>​
 <​b>​Year</​b>:​ 2015 <br> <​b>​Year</​b>:​ 2015 <br>
 <​b>​SN</​b>:​ 3851002396<​br>​ <​b>​SN</​b>:​ 3851002396<​br>​
 +&nbsp <br>
 +Data will be deleted after: <b>15 days</​b>​
 &nbsp <br> &nbsp <br>
 &nbsp <br> &nbsp <br>
 &nbsp <br> &nbsp <br>
-&rarr; <a href="​https://​my.agendo.science/​calendar/?​id=MjZjYWxlbmRhcnM="><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=date.png"> ​ Zeiss Cell Observer Booking</​a>​ 
- <​br> ​ 
 &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>​ &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>​
  <​br>​  <​br>​
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 ===== Microscope overview ===== ===== Microscope overview =====
-{{  :​widefield_lightpath.png?​0x300}}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 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]].+{{  :​widefield_lightpath.png?​0x300}}The Zeiss Cell Observer is a fully motorized inverted //widefield fluorescence microscope//​ ideal for live-cell imaging ​with fast acquisition speeds. It is equipped with a large cage incubator and a stage top incubator for temperature control and CO2 supply and with Definite Focus for hardware focus control during long time-lapse acquisitions. Using the ZEN software you can control the motorized filters, shutters and stage to simultaneously set up multi-color time-lapse imaging experiments in multiple stage positions. The stage is furthermore equipped with a piezo for fast Z displacement. You can choose between a HXP metal halide lamp or fast-switching LEDs for illumination. Its cooled ​[[https://​asset-downloads.zeiss.com/​catalogs/​download/​mic/​a8e5b4d7-25f6-4069-8f03-c6713d044c87/​EN_product-info_Axiocam-506_mono.pdf|Axiocam 506m]] camera allows you to capture weak fluorescent signals and minimize photobleaching/​photodamage in light sensitive samples. ​It is also equipped with a high sensitivity ​[[https://www.photometrics.com/products/prime-family/primebsiexpress|Photometrics Prime BSI Express]] sCMOS camera for high resolution ​imaging with maximized signal detection.
  
-  * **Microscope**:​ [[http://​www.zeiss.com/​microscopy/​en_de/products/light-microscopes/axio-observer-for-biology.html|Zeiss ​Axio Observer]] +  * **Microscope**: Zeiss Axio Observer 
-  * **Camera**: [[https://www.zeiss.com/microscopy/int/products/microscope-cameras/axiocam-506-mono.html|Axiocam 506 mono CCD]]+  * **LED Illumination**: [[https://​www.zeiss.com/​microscopy/​en/products/accessories/colibri.html|Zeiss ​Colibri 7]] 
 +  * **Camera** ​(left port): [[https://asset-downloads.zeiss.com/catalogs/download/mic/a8e5b4d7-25f6-4069-8f03-c6713d044c87/EN_product-info_Axiocam-506_mono.pdf|Axiocam 506 mono CCD]] 
 +  * **Camera** (right port): [[https://​www.photometrics.com/​products/​prime-family/​primebsiexpress|Photometrics Prime BSI Express sCMOS]]
  
-{{: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.+{{::​phenocycler.png?260  ​|}}This system ​is also set up to work together with the [[https://​www.youtube.com/​watch?​v=OQGJX45Wsgw|AKOYA PhenoCycler]] fluidics instrument for automated iterative imaging cycles of whole slide tissues for [[https://​www.akoyabio.com/​why-spatial-biology/​|Spatial Biology]] applications,​ such as image-based quantification of biomarkers to predict immunotherapy response, or quantification of cells by lineage and variant with single-cell resolution in the context of an intact tissue sample.
  
-===== Booking Rules ===== +  * [[https://​www.youtube.com/​watch?​v=OQGJX45Wsgw|Understanding the PhenoCycler Technology]] ​ 
-The Zeiss Cell Observer booking is divided in three daily slots: +  ​* [[https://​www.akoyabio.com/​webinar/​a-beginners-guide-to-codex/|A Beginner’s Guide to CODEX]] 
- 9:00 to 13:​00  ​|  ​13:00 to 17:​00  ​ 17:00 to 21:00  |+  * [[https://​www.akoyabio.com/​webinar/​spatial-phenotyping-a-revolutionary-approach-to-biomarker-discovery-for-cancer-immunotherapy/​|Spatial PhenotypingA Revolutionary Approach ​to Biomarker Discovery for Cancer Immunotherapy]]
  
-  ​**user** can book at maximum **2 sessions ​per week** +{{:​warning.png?​25|}} Data files older than **15 days** will be automatically deleted on this system, please copy your data to the iMM server using the desktop link. 
-  - 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** +===== Booking Rules ===== 
-  - The above rules do not apply for sessions booked on the very same day or **24 hours ahead**+  ​- **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]]**.   - 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 ===== ===== System components =====
 +
 +==== LEDs  ====
 +^  Line  ^  Wavelength ​ ^
 +|  UV  |  385 nm  |
 +|  B  |  475 nm  |
 +|  G  |  555 nm  |
 +|  Y  |  590 nm  |
 +|  R  |  630 nm  |
  
 ==== Filtersets ==== ==== Filtersets ====
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 |  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  |  495 nm  |  500-550 nm  | |  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  |  495 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 nm  |  570-640 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 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  |  ​395 nm  |  ​420-470 nm  | +|  3  |  ​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  |  ​660 nm  |  ​665-715 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  |  ​660 nm  |  ​665-715 nm  ​+|  4  |  ​Analyzer DIC  ||||| 
-|  5  |  Empty  ||||| +|  5  |  QUAD  |  [[https://​www.micro-shop.zeiss.com/​en/​us/​shop/​filterAssistant/​filtersets/​489090-9100-000|FS90HE]] |  370-400 nm  |  405 nm  |  410-440 nm  | 
-|  6  |  Empty  |||||+|  :::  |  :::  |  :::  |  450-488 nm  |  493 nm  |  499-529 nm  | 
 +|  :::  |  :::  |  :::  |  540-570 nm  |  575 nm  |  580-605 nm  | 
 +|  :::  |  :::  |  :::  |  615-648 nm  |  653 nm  |  659-759 nm  | 
 +|  6  |  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  |  ​395 nm  |  ​420-470 nm  |
  
 ==== Objectives ==== ==== Objectives ====
 ^  Magnification ​ ^  Model  ^  Immersion ​ ^  NA  ^  WD (mm)  ^  Reference ​ ^ ^  Magnification ​ ^  Model  ^  Immersion ​ ^  NA  ^  WD (mm)  ^  Reference ​ ^
 |  10x  |  EC Plan-Neofluar Ph1  |  Air  |  0.30  |  5.20  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420341-9911-000/​Objective-EC-Plan-Neofluar-10x-0.30-Ph1-M27|420341-9911-000]] ​ | |  10x  |  EC Plan-Neofluar Ph1  |  Air  |  0.30  |  5.20  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420341-9911-000/​Objective-EC-Plan-Neofluar-10x-0.30-Ph1-M27|420341-9911-000]] ​ |
-|  20x  |  EC Plan-Neofluar Ph 2  |  Air  |  0.50  |  2.00  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​440341-9904-000/​Objective-EC-Plan-Neofluar-20x-0.5-Ph2|440341-9904-000]] ​ | 
 |  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]] ​ | |  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]] ​ |
 +|  20x  |  EC Plan-Neofluar Ph 2  |  Air  |  0.50  |  2.00  |  [[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  |  EC Plan-NeoFluar ​ |  Air  |  0.75  |  0.71  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420360-9900-000/​Objective-EC-Plan-Neofluar-40x-0.75-M27|420360-9900-000]] ​ | |  40x  |  EC Plan-NeoFluar ​ |  Air  |  0.75  |  0.71  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420360-9900-000/​Objective-EC-Plan-Neofluar-40x-0.75-M27|420360-9900-000]] ​ |
 |  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]] ​ | |  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]] ​ |
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 |  5x  |  EC Plan-NeoFluar ​ |  Air  |  0.16  |  18.50  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420330-9901-000/​Objective-EC-Plan-Neofluar-5x-0.16-M27|420330-9901-000]] ​ | |  5x  |  EC Plan-NeoFluar ​ |  Air  |  0.16  |  18.50  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420330-9901-000/​Objective-EC-Plan-Neofluar-5x-0.16-M27|420330-9901-000]] ​ |
 |  10x  |  EC Plan-Neofluar ​ |  Air  |  0.30  |  5.20  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420340-9901-000/​Objective-EC-Plan-Neofluar-10x-0.30-M27|420340-9901-000]] ​ | |  10x  |  EC Plan-Neofluar ​ |  Air  |  0.30  |  5.20  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420340-9901-000/​Objective-EC-Plan-Neofluar-10x-0.30-M27|420340-9901-000]] ​ |
 +|  25x  |  LCI Plan-Neofluar Corr DIC  |  Oil/​Glyc/​W ​ |  0.80  |  0.21  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420852-9973-000/​Objective-LCI-Plan-Neofluar-25x-0.8-Imm-Corr-DIC-M27|420852-9972-000]] ​ |
 |  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-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]] ​ | |  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]] ​ |
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 ^  Model  ^  Type  ^  Frame Size  ^  Pixel Size (µm)  ^ ^  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  | |  [[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 ===== ===== System Turn On Procedures =====
-  ​* Turn on the HXP 120 fluorescent light source+ 
 +  ​* Turn on the HXP 120 fluorescent light source ​(if used)
 {{zeiss_axio_observer_hxp.jpg?​120|}} {{zeiss_axio_observer_hxp.jpg?​120|}}
-  * Turn on the temperature and CO2 controller (if you need them). +  * Turn on the temperature and CO2 controller ​- white power strip (if you need them). 
-{{zeiss_axio_observer_temp.jpg?​80|}} +  * If you need CO2, open the Cell Observer CO2 valve 
-  * If you need CO2, open the valve +  * Turn on the motorized stage controller (**1** on remote control)
-{{zeiss_axio_observer_co2.jpg?​80|}} +
-  * Turn on the motorized stage controller (**A** on remote control)+
 {{zeiss_axio_observer_a.jpg?​height=150|}} {{zeiss_axio_observer_a.jpg?​height=150|}}
-  ​* Turn on the Definite Focus controller (if you are going to use it) +  * Turn on the microscope power supply (**2** on remote control)
-{{zeiss_axio_observer_df.jpg?​height=150|}} +
-  ​* Turn on the microscope power supply (**B** on remote control)+
 {{zeiss_axio_observer_b.jpg?​height=150|}} {{zeiss_axio_observer_b.jpg?​height=150|}}
   * Turn on the computer   * Turn on the computer
-  * Log in to Windows ​(Biomaging User).+  * Login in to Windows ​with your Agendo credentials
   * Start the **ZEN** software   * Start the **ZEN** software
 +  * Select HXP or LED Workspace in ZEN (top left)
 +{{::​workspace_selection.png?​250|}}
  
-===== Microscope ​Turn Off procedures =====+===== System ​Turn Off procedures =====
 If there is another user for this microscope is the __next hour__: If there is another user for this microscope is the __next hour__:
   * Leave the fluorescent light source on   * Leave the fluorescent light source on
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 {{:​cell_observer_pc_vs_ups.png?​250|}} {{:​cell_observer_pc_vs_ups.png?​250|}}
   * Clean up immersion objectives   * Clean up immersion objectives
-  * Turn off the microscope power supply (**B** on remote control+  * Turn off the microscope power supply (**2** on remote control) 
-  * Turn off the Definite Focus controller (if used+  * Turn off the motorized stage controller (**1** on remote control) 
-  * Turn off the motorized stage controller (**A** on remote control) +  * Turn off the Temperature and CO2 controller ​- white power strip (if used) 
-  * Turn off the Temperature and CO2 controller (if used) +  * Close the Cell Observer CO2 valve (if used) 
-  * Turn off the HXP 120 fluorescent light source+  * Turn off the HXP 120 fluorescent light source ​(if used)
  
 ---- ----
-[[resources|Back to the Resources ​page]]+[[resources|Back to the Equipment ​page]]
zeiss_cell_observer.1594258913.txt.gz · Last modified: 2020/07/09 03:41 by bioimaging