User Tools

Site Tools


zeiss_cell_observer_sd

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
zeiss_cell_observer_sd [2018/06/07 10:59]
bioimaging
zeiss_cell_observer_sd [2021/01/17 04:43] (current)
bioimaging [Microscope Turn Off Procedure]
Line 1: Line 1:
 <​html>​ <​html>​
-<img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_name.jpg">+<img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_name_new.png">
 <table style="​border:​0px solid white;">​ <table style="​border:​0px solid white;">​
 <tr style="​border:​0px solid white;">​ <tr style="​border:​0px solid white;">​
 <td style="​border:​0px solid white;">​ <td style="​border:​0px solid white;">​
-<a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_wiki.jpg"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_wiki.jpg" width=300></​a>​+<a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_wiki_new.png"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_wiki_new.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>:​ Room P2-A-22 (<img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=telephone_icon.gif" width=15>​ 47217) <​br> ​+<​b>​Location</​b>: ​<a href="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=zeiss_cell_observer_sd_map_new.png">​Room P2-A-22</​a> ​(<img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=phone_neg.png" width=15>​ 47217) <​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">​Carl Zeiss Microimaging</​a><​br>​
-<​b>​Model</​b>: ​<a href="​http://​www.zeiss.com/​microscopy/​en_de/​products/​confocal-microscopes/​cell-observer-sd-for-biology.html"​ target="​_blank">​Cell Observer SD</a><br>+<​b>​Model</​b>:​ Cell Observer SD<​br>​
 <​b>​Nickname</​b>:​ "Cell Observer SD"<​br>​ <​b>​Nickname</​b>:​ "Cell Observer SD"<​br>​
-<​b>​Software</​b>:​ ZEN<​br>​+<​b>​Software</​b>:​ ZEN 2.6 (blue edition)<br>
 <​b>​Year</​b>:​ 2015 <br> <​b>​Year</​b>:​ 2015 <br>
 <​b>​SN</​b>:​ 3851001637 <br> <​b>​SN</​b>:​ 3851001637 <br>
Line 16: Line 16:
 &nbsp <br> &nbsp <br>
 &nbsp <br> &nbsp <br>
-&rarr; <a href="​https://​imm.medicina.ulisboa.pt/​intranet/booking/119"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=date.png"> ​ Zeiss Cell Observer SD Booking</​a>​+&rarr; <a href="​https://​my.agendo.science/calendar/?​id=MjVjYWxlbmRhcnM="><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=date.png"> ​ Zeiss Cell Observer SD Booking</​a>​
  <​br> ​  <​br> ​
 &rarr; <a href="/​facility/​bioimaging/​doku.php?​id=zeiss_cell_observer_sd_quality"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=list-icon.png"​ width=18>​ Zeiss Cell Observer SD Quality Control</​a>​ &rarr; <a href="/​facility/​bioimaging/​doku.php?​id=zeiss_cell_observer_sd_quality"><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=list-icon.png"​ width=18>​ Zeiss Cell Observer SD Quality Control</​a>​
Line 30: Line 30:
 ===== System overview ===== ===== System overview =====
  
-{{  :​spinning_disk.jpg?0x300|}} The Zeiss Cell Observer SD //spinning disk confocal microscope//​ is a fast imaging system which provides a trade-off between confocality,​ resolution and speed. It is an inverted microscope ideal for live cell applications which require fast acquisition speeds rather than high resolution images. The scanning unit achieves confocality by directing light through a spinning disk with many small pinholes. Images are then acquired with a sensitive EMCCD which allows for very small exposure times but is limited in resolution to 512x512 pixels. The stage is motorized and furthermore equipped with a piezo for Z displacement so fast 4D imaging is possible in multiple stage positions. The system is also equipped with a large size incubator for temperature control, a small stage incubator for CO2 supply and with Definite Focus for hardware focus control during ​long time-lapse acquisitions. You can also use the system as a widefield microscope, using a sCMOS camera for acquisition. Even though its resolution is not as high as a //​point-scanning confocal system// such as the [[zeiss_lsm_880|Zeiss LSM 880]] or [[zeiss_lsm_710|Zeiss LSM 710]], it is much faster ​than these two systems. You can also check the [[3i_marianas_sdc|3i Marianas SDC]] if you need a spinning disk with higher laser power illumination. If your personal computer cannot handle all the data you collected, check out the [[big_guy|Big Guy]] or [[colossus|Colossus]].+{{  :​spinning_disk.png|}} The Zeiss Cell Observer SD //spinning disk confocal microscope//​ is a fast imaging system which provides a trade-off between confocality,​ resolution and speed. It is an inverted microscope ideal for live cell applications which require fast acquisition speeds rather than high resolution images. The scanning unit achieves confocality by directing light through a spinning disk with many small pinholes. Images are then acquired with a sensitive EMCCD which allows for very small exposure times but is limited in resolution to 512x512 pixels. The stage is motorized and furthermore equipped with a piezo for Z displacement so fast 4D imaging is possible in multiple stage positions. The system is also equipped with a large size incubator for temperature control, a stage top incubator for CO2 supply and with Definite Focus.2 for hardware focus control during ​large tile or multi-position/​time-lapse acquisitions ​(check tutorial videos below). You can also use the system as a widefield microscope, using fast-swicthing LEDs for illumination (Zeiss Colibri.2) and a sCMOS camera for acquisition. Even though its resolution is not as high as a //​point-scanning confocal system// such as the [[zeiss_lsm_710|Zeiss LSM 710]], it is much faster. You can also check the [[3i_marianas_sdc|3i Marianas SDC]] if you need a spinning disk with higher laser power illumination. If your personal computer cannot handle all the data you collected, check out the [[big_guy|Big Guy]] or [[colossus|Colossus]].
  
   * **Microscope**:​ [[http://​www.zeiss.com/​microscopy/​en_de/​products/​light-microscopes/​axio-observer-for-biology.html|Zeiss Axio Observer]]   * **Microscope**:​ [[http://​www.zeiss.com/​microscopy/​en_de/​products/​light-microscopes/​axio-observer-for-biology.html|Zeiss Axio Observer]]
-  * **Confocal scanner**: [[http://www.andor.com/microscopy_systems/peripherals/confocal_scanners/|Yokogawa CSU-x1]] +  * **Confocal scanner**: [[https://www.yokogawa.com/eu/solutions/products-platforms/​life-science/​spinning-disk-confocal/​csu-x1-confocal-scanner-unit/|Yokogawa CSU-x1]] 
-  * **EMCCD Camera**: [[http://​www.photometrics.com/​products/emccdcams/evolve/512.php|Evolve 512 EMCCD]] +  * **EMCCD Camera**: [[https://​www.photometrics.com/​wp-content/uploads/2019/10/​Evolve512-Datasheet.pdf|Evolve 512 EMCCD]] 
-  * **sCMOS Camera**: [[http://​www.hamamatsu.com/​eu/en/community/life_science_camera/​product/​search/​C11440-22CU/index.html|Hamamatsu ORCA-flash4.0 V2]]+  * **sCMOS Camera**: [[https://​www.hamamatsu.com/​resources/pdf/sys/SCAS0081E_C11440-22CU.pdf|Hamamatsu ORCA-flash4.0 V2]] 
 +  * [[https://​www.zeiss.com/​microscopy/​int/​products/​light-microscopes/​axio-observer-for-biology/​definite-focus.html|Definite Focus.2]] 
 +    * | [[https://​www.youtube.com/​watch?​v=Che0bouWcVE|Introduction to Definite Focus.2]] 
 +    * | [[https://​www.youtube.com/​watch?​v=I_c3SAHF984|Perform Large Tile Experiments with Definite Focus.2]] 
 +    * | [[https://​www.youtube.com/​watch?​v=IUvdvSNsE1I|Multi-Position Experiments with Definite Focus.2]] 
 +    * | [[https://​www.youtube.com/​watch?​v=DqqV6cs3mZg|Multi-Position Time Series with Definite Focus.2]]
  
-{{warning.jpg?20|}} 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.+{{: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 =====
 +  - **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]]**.
 + 
 ===== System components ===== ===== System components =====
  
Line 50: Line 60:
 ==== Objectives ==== ==== Objectives ====
  
-{{:​zeiss_cell_observer_sd_objectives.jpg ​ |}} +^  Magnification ​  ​^ ​ Model  ^  ​Immersion ​ ​^ ​ NA  ^  WD (mm)  ​^ ​ Reference ​ ^ 
-^  Magnification ​  ​^ ​ Model  ^  ​Type  ​^ ​ NA  ^  WD (mm)  ^ +|  ​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  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=42373720ae8af6&​l=en&​p=us&​f=o&​a=v&​m=s&​id=420651-9911-000|Plan-Apochromat]]  |  ​Dry  ​| ​ 0. ​| ​ 0.55  | +|  ​20x  |  Plan-Apochromat Ph2  |  Air  ​| ​ 0.80  ​| ​ 0.55  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420651-9911-000/​Objective-Plan-Apochromat-20x-0.8-Ph2-M27|420651-9911-000]] ​ | 
-|  40x  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=42373720ae8af6&​l=en&​p=us&​f=o&​a=v&​m=s&​id=421867-9970-000|LD C-Apochromat]]  ​| ​ Water  |  1.10  |  0.62  | +|  40x  |  ​LD C-Apochromat ​Corr  ​| ​ Water  |  1.10  |  0.62  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​421867-9970-000/​Objective-LD-C-Apochromat-40x-1.1-W-Corr-M27|421867-9970-000]]  | 
-|  40x  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=42373720ae8af6&​l=en&​p=us&​f=o&​a=v&​m=s&​id=420762-9900-000|Plan-Apochromat]] ​ |  Oil  |  1.40  |  0.13  | +|  40x  |  Plan-Apochromat DIC  ​| ​ Oil  |  1.40  |  0.13  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420762-9900-000/Objective-Plan-Apochromat-40x-1.4-Oil-DIC-M27|420762-9900-000]]  | 
-|  63x  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=3407786617d462&​l=en&​p=uk&​f=o&​a=v&​m=s&​id=420782-9900-000|Plan-Apochromat]] ​ |  Oil  |  1.40  |  0.19  | +|  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  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=4238899732b41f&​l=en&​p=us&​f=o&​a=v&​m=s&​id=420781-9910-000|Plan-Apochromat ​Ph3]]  |  Oil  |  1.40  ​| ​ 0.19  | +|  100x  |  α Plan-Apochromat DIC  ​| ​ Oil  |  1.46  ​| ​ 0.11  ​| ​ [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420792-9800-000/Objective-alpha-Plan-Apochromat-100x-1.46-Oil-DIC-M27|420792-9800-000]] ​ |
-|  100x  ​| ​ [[https://​www.micro-shop.zeiss.com/​?​s=7138707e1a1de&​l=en&​p=uk&​f=o&​a=v&​m=s&​id=420792-9800-000|alpha Plan-Apochromat]]  |  Oil  |  ​1.46   ​0.11 ​ |+
  
-<​html>​ +**Upon request:** 
-<br> +^  Magnification ​ ^  Model  ^  Immersion ​ ^  NA  ^  WD (mm)  ^  Reference ​ ^ 
-<br> +|  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]] ​ | 
-<​br>​ +|  25x  |  LCI Plan-Neofluar Corr DIC  |  Oil/​Glyc/​W ​ |  0.80  |  0.21  |  [[https://​www.micro-shop.zeiss.com/​en/​de/​shop/​objectives/​420852-9972-000/Objective-LCI-Plan-Neofluar-25x-0.8-Imm-Corr-DIC-M27|420852-9972-000]] ​ |
-<​br>​ +
-</html>+
  
 ==== Filtersets (Widefield) ==== ==== Filtersets (Widefield) ====
  
-{{:zeiss_cell_observer_sd_filters_widefield.jpg  |}}+^  Position ​ ^  Filterset ​ ^  Reference ​ ^  Excitation ​ ^  Dichroic ​ ^  Emission ​ ^ 
 +|  1  |  Green  |  [[https://www.micro-shop.zeiss.com/?​s=7139069fdc79c&​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  |  Red  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​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  |  Blue  |  [[https://​www.micro-shop.zeiss.com/?​s=163176628fcf844&​l=en&​p=us&​f=f&​a=v&​b=f&​id=488049-9901-000&​o=|FS49]] ​ |  335-383 nm  |  395 nm  |  420-470 nm  | 
 +|  4  |  Far Red  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​l=en&​p=us&​f=f&​a=v&​b=f&​id=488050-9901-000&​o=|FS50]] ​ |  625-655 nm  |  660 nm  |  665-715 nm  | 
 +|  5  |  QUAD  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​l=en&​p=us&​f=f&​a=v&​b=f&​id=489081-9010-000&​o=| ​ FS81HE]] ​ |  357-393 nm  |  400 nm  |  407-412 nm  | 
 +|  :::  |  :::  |  :::  |  473-496 nm  |  503 nm  |  511-528 nm  | 
 +|  :::  |  :::  |  :::  |  545-562 nm  |  570 nm  |  577-602 nm  | 
 +|  :::  |  :::  |  :::  |  620-642 nm  |  650 nm  |  658-704 nm  | 
 +|  6  |  Empty  |||||
  
-^  Position ​ ^  Filterset ​ ^  Reference ​ ^  Excitation ​ ^  Emission ​ ^ +==== Emission ​Filters ​(Confocal) ====
-|  1  |  Green  |  [[https://​www.micro-shop.zeiss.com/?​s=7139069fdc79c&​l=en&​p=us&​f=f&​a=v&​b=f&​id=489038-9901-000&​o=|FS38HE]] ​ |  450-490 nm  |  500-550 nm  | +
-|  2  |  Red  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​l=en&​p=us&​f=f&​a=v&​b=f&​id=489043-9901-000&​o=|FS43HE]] ​ |  538-562 nm  |  570-640 nm  | +
-|  3  |  Blue  |  [[https://​www.micro-shop.zeiss.com/?​s=163176628fcf844&​l=en&​p=us&​f=f&​a=v&​b=f&​id=488049-9901-000&​o=|FS49]] ​ |  335-383 nm  |  420-470 nm  | +
-|  4  |  Far Red  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​l=en&​p=us&​f=f&​a=v&​b=f&​id=488050-9901-000&​o=|FS50]] ​ |  625-655 nm  |  665-715 nm  | +
-|  5  |  QUAD  |  [[https://​www.micro-shop.zeiss.com/?​s=4237481102cf7b&​l=en&​p=us&​f=f&​a=v&​b=f&​id=489081-9010-000&​o=| ​ FS81HE]] ​ |  357-393 nm  |  407-412 nm  | +
-|  :::  |  :::  |  :::  |  473-496 nm  |  511-528 nm  | +
-|  :::  |  :::  |  :::  |  545-562 nm  |  577-602 nm  | +
-|  :::  |  :::  |  :::  |  620-642 nm  |  658-704 nm  | +
-|  6  |  none  |  |  |  | +
- +
-<​html>​ +
-<​br>​ +
-</​html>​ +
- +
-==== Emission ​Filtersets ​(Confocal) ==== +
- +
-{{:​zeiss_cell_observer_sd_filters_confocal.jpg ​ |}}+
  
 ^  Position ​ ^  Transmission ​ ^ ^  Position ​ ^  Transmission ​ ^
Line 98: Line 97:
 |  5: BP 600 50  |  575-625 nm  | |  5: BP 600 50  |  575-625 nm  |
 |  6: BP 690/​50 ​ |  665-715 nm  | |  6: BP 690/​50 ​ |  665-715 nm  |
 +
 +==== Cameras ====
 +^  Model  ^  Type  ^  Frame Size  ^  Pixel Size (µm)  ^  Quantum Efficiency ​ ^
 +|  [[https://​www.photometrics.com/​wp-content/​uploads/​2019/​10/​Evolve512-Datasheet.pdf|Photometrics Evolve 512]]  |  EMCCD  |  512 x 512  |  16 x 16  |  > 90%  |
 +|  [[https://​www.hamamatsu.com/​resources/​pdf/​sys/​SCAS0081E_C11440-22CU.pdf|Hamamatsu ORCA-flash4.0 V2]]  |  sCMOS  |  2048 x 2048  |  6.5 x 6.5  |  82%  |
 +
 +===== Microscope Turn On Procedure =====
 +  * Turn on the computer
 +  * Login in to Windows (Bioimaging User)
 +  * Turn on the black socket outlet **number 1** underneath the microscope table
 +{{::​sd_power.png?​200|}}
 +  * Wait for the Definite Focus controller to show the App-Ver. and OS-Image info
 +{{::​df_on.png?​500|}}
 +  * Turn on the black socket outlet **number 2** underneath the microscope table
 +  * Turn on the black socket outlet **number 3** underneath the microscope table (for spinning disk mode)
 +  * Start the **ZEN Blue** software
 +
 +**Warning**:​ If you need to change the stage adapter, please contact the <​html><​a href="/​facility/​bioimaging/​doku.php?​id=about">​Bioimaging Unit</​a>​ (<​b>​imm-bioimaging@medicina.ulisboa.pt</​b>​ | <img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=phone_neg.png"​ width=15>​ 47222</​html>​)
 +
 +===== Microscope Turn Off Procedure =====
 +If there is another user for this microscope in the __next hour__:
 +  * Exit the **ZEN** software, leave the lasers on
 +  * Log off the computer
 +  * Clean up immersion objectives
 +Else:
 +  * Exit the **ZEN** software
 +  * Shut down the computer
 +  * Clean up immersion objectives
 +  * Turn off the black socket outlets underneath the microscope table by reverse order (3→2→1)
  
 ---- ----
  
-[[resources|Back to the Resources ​page]]+[[resources|Back to the Equipment ​page]]
zeiss_cell_observer_sd.1528361956.txt.gz · Last modified: 2018/06/07 10:59 by bioimaging