zeiss_cell_observer
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zeiss_cell_observer [2020/02/29 10:47] bioimaging [Microscope overview] |
zeiss_cell_observer [2024/01/31 10:47] 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 2 (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> | ||
| + |   <br> | ||
| + | Data will be deleted after: <b>15 days</b> | ||
|   <br> |   <br> | ||
|   <br> |   <br> | ||
|   <br> |   <br> | ||
| - | → <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> | ||
| - | <br> | ||
| → <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> | → <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 Phenotyping: A Revolutionary Approach to Biomarker Discovery for Cancer Immunotherapy]] |
| - | - A **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 ==== | ||
| - | ^ Position ^ Filterset ^ Reference ^ Excitation ^ Emission ^ | + | ^ Position ^ Filterset ^ Reference ^ Excitation ^ Dichroic ^ 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 | | + | | 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 | 570-640 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 | 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 | 665-715 nm | | + | | 4 | Analyzer DIC ||||| |
| - | | 5 | none | none | none | none | | + | | 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 | none | none | none | none | | + | | ::: | ::: | ::: | 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 | 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]] | | + | | 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 | 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]] | | ||
| - | | 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]] | | + | | 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]] | | ||
| | 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]] | | ||
| + | | 63x | Plan-Apochromat Ph3 | Oil | 1.40 | 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]] | | ||
| **Upon request:** | **Upon request:** | ||
| ^ Magnification ^ Model ^ Immersion ^ NA ^ WD (mm) ^ Reference ^ | ^ 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]] | | + | | 1.25x | EC Epiplan-Neofluar | Air | 0.035 | 4.00 | [[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]] | | + | | 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]] | |
| - | | 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]] | | + | | 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]] | | ||
| - | | 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]] | | | 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]] | | ||
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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 ===== | ===== Microscope Turn Off procedures ===== | ||
| Line 104: | Line 119: | ||
| {{: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.txt · Last modified: 2024/04/01 23:50 by bioimaging
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