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--- zeiss_lsm_980_oeiras [2025/03/01 01:38]
bioimaging [Detector(s)]
+++ zeiss_lsm_980_oeiras [2025/12/11 23:53] (current)
bioimaging [Filtersets (for eyepieces)]
@@ Line 6: / Line 6: @@
 <a href="/facility/bioimaging/lib/exe/fetch.php?media=lsm_980.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=lsm_980.jpg" width=300></a>
 <td style="border:0px solid white;"> <p style="line-height:1.8">
-<b>Location</b>: [Oeiras] Room 0B06<br>
+<b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=bartolomeu_dias_wing_2025_-_zeiss_lsm_980.png">[Oeiras] Room 0B06</a><br>
 <b>Manufacturer</b>: <a href="http://www.zeiss.de/micro" target="_blank">ZEISS Microscopy</a><br>
@@ Line 13: / Line 13: @@
 <b>Nickname</b>: "980"<br>
-<b>Software</b>: Zen blue v3.3 <br>
+<b>Software</b>: ZEN 3.12 <br>
-<b>Year</b>: 2019  <br>
+<b>Year</b>: 2019<br>
-<b>SN</b>:  <br>
+<b>SN</b>: 2871000107<br>
 &nbsp <br>
 Data will be deleted after: <b>1 month</b>
@@ Line 31: / Line 31: @@
 ===== Microscope overview =====
-{{  :confocal_pinhole.png?340}} The Zeiss LSM 980 with Airyscan 2 is a [[https://www.youtube.com/watch?v=rTkjQ6Q0p5I|point scanning confocal microscope]] is an inverted microscope equipped with a laser scanning head with a total of 6 PMT/GaAsp + 1 Airyscan detectors. The Airyscan can achieve non-diffraction limited optical sectioning with resolutions down to 140nm laterally and ~400nm axially. It also allows acquisition in “Multiplexing” mode(s), which accelerate the acquisition speed (4/8x faster) or in sensitivity mode that enhances the signal-to-noise acquisition.
+{{  :confocal_pinhole.png?340}} The Zeiss LSM 980 with Airyscan 2 is an inverted [[https://www.youtube.com/watch?v=rTkjQ6Q0p5I|point scanning confocal microscope]] equipped with a laser scanning head with a total of 6 PMT/GaAsp + 1 Airyscan detectors. The Airyscan can achieve non-diffraction limited optical sectioning with resolutions down to 140nm laterally and ~ 400nm axially. It also allows acquisition in “Multiplexing” modes, which accelerate the acquisition speed (4/8x faster) or in sensitivity mode that enhances the signal-to-noise acquisition.
-The microscope is also equipped with a dark heating and atmospheric control chamber to allow live imaging of mammalian cells (O2 control is also possible, upon request). We have available an objective inverter for some intra-vital or open-dish applications (upon request only, requires preparation).
+The microscope is equipped with a dark large cage incubator and atmospheric control chamber to allow live imaging of mammalian cells (O2 control is also possible, upon request). We have available an objective inverter for some intra-vital or open-dish applications (upon request only, requires preparation).
   * **Microscope**: [[https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html|Zeiss Axio Observer]]
@@ Line 51: / Line 51: @@
 {{:warning.png?25|}} Data files older than **1 month** will be automatically deleted on this system, please copy your data to the GIMM 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 =====
-==== Lasers =====
+==== LASERs =====
-^  Laser ^  Excitation line  ^  Power  ^  Description (use)   ^
+^  LASER  ^  Wavelength  ^  Maximum Power  ^
-|  <fc #ff00ff>405 nm (violet)</fc>  |  405 nm  |  15 mW  |  <fc #00ffff>DAPI, Hoechst</fc>   |
+|  Violet  |  <fc #a600ff>405 nm</fc>  |  15 mW  |
-|  <fc #6495ed>488 nm (blue)</fc>  |  488 nm  |  13 mW  |  <fc #00ff00>GFP, FITC, Alexa488</fc>   |
+|  Blue  |  <fc #00f7ff>488 nm</fc>  |  13 mW  |
-|  <fc #00ff00>561 nm (green)</fc>  |  561 nm  |  13 mW  |  <fc #ffa500>RFP, TRITC, Cy3, Dylight Orange</fc>   |
+|  Yellow-green  |  <fc #c6ff00>561 nm</fc>  |  13 mW  |
-|  <fc #ff0000>639 nm (red)</fc>  |  639 nm  |  10 mW  |  <fc #cd5c5c>Cy5, APC, Alexa/ATTO633-647</fc>   |
+|  Red  |  <fc #ff2600>639 nm</fc>  |  10 mW  |
-If you require more laser lines (eg, 445nm - CFP/Cerulean, 514nm - YFP, or 594nm mCherry/AF594), we suggest as an alternative the LSM980-32 in Lisbon:
+If you require more laser lines (e.g., <fc #0028ff>445 nm</fc>, <fc #1aff00>514 nm</fc>, or <fc #ffd200>594 nm</fc>), we suggest as an alternative the [[https://imm.medicina.ulisboa.pt/facility/bioimaging/doku.php?id=zeiss_lsm_980-32|[Lisbon] ZEISS LSM 980-32 with Airyscan 2]].
-https://imm.medicina.ulisboa.pt/facility/bioimaging/doku.php?id=zeiss_lsm_980
+==== Filtersets (for eyepieces) ====
+^  Filterset  ^  Excitation  ^  Dichroic  ^  Emission  ^  Reference  ^
+|  Blue  |  G 365 nm  |  395 nm  |  <fc #0028ff>420-470 nm</fc>  |  [[https://www.micro-shop.zeiss.com/?s=163176628fcf844&l=en&p=us&f=f&a=v&b=f&id=488049-9901-000&o=|FS49]]  |
+|  Green  |  450-490 nm  |  493 nm  |  <fc #4aff00>500-550 nm</fc>  |  [[https://www.micro-shop.zeiss.com/?s=7139069fdc79c&l=en&p=us&f=f&a=v&b=f&id=489038-9901-000&o=|FS38HE]]  |
+|  Red  |  533-558 nm  |  570 nm  |  <fc #ffad00>570-640 nm</fc>  |  [[https://www.micro-shop.zeiss.com/?s=163176628fcf844&l=en&p=us&f=f&a=v&b=f&id=000000-1114-101&o=|FS43]]  |
 ==== Objectives ====
 ^  Magnification   ^  Model  ^  Immersion  ^  NA  ^  WD (mm)  ^  Reference  ^
-|  2.5x  |    |  -  |  0.085  |  8.8  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420320-9902-000/Objective-EC-Plan-Neofluar-2.5x-0.085-M27|420320-9902-000]]  |
+|  <fc #c2a446>2.5x</fc>  |    |  -  |  0.085  |  8.8  |  [[https://www.micro-shop.zeiss.com/en/us/shop/objectives/420320-9902-000/Objective-EC-Plan-Neofluar-2.5x-0.085-M27|420320-9902-000]]  |
-|  10x  |  EC Plan-Neofluar  |  Air  |  0.45  |  2.0  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420640-9900-000/Objective-Plan-Apochromat-10x-0.45-M27|420640-9900-000]]  |
+|  <fc #fef042>10x</fc>  |  EC Plan-Neofluar  |  Air  |  0.45  |  2.0  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420640-9900-000/Objective-Plan-Apochromat-10x-0.45-M27|420640-9900-000]]  |
-|  20x  |  Plan-Apochromat  |  Air  |  0.75  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420150-9900-000/Objective-Fluar-20x-0.75-M27|420150-9900-000]]  |
+|  <fc #0aa05c>20x</fc>  |  Plan-Apochromat  |  Air  |  0.75  |  0.55  |  [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420150-9900-000/Objective-Fluar-20x-0.75-M27|420150-9900-000]]  |
-|  25x  |    |  W/Sil/Gly/Oil*  |  0.80  |  0.57  |   [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420852-9870-790/Objective-LD-LCI-Plan-Apochromat-25x-0.8-Imm-autocorr-DIC-M27|420852-9870-790]]  |
+|  <fc #0aa05c>25x</fc>  |    |  W/Sil/Gly/Oil *  |  0.80  |  0.57  |   [[https://www.micro-shop.zeiss.com/en/ee/shop/objectives/420852-9870-790/Objective-LD-LCI-Plan-Apochromat-25x-0.8-Imm-autocorr-DIC-M27|420852-9870-790]]  |
-|  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]] |
+|  <fc #01b3f5>40x</fc>  |  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]] |
-|  63x  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420782-9900-799/Objective-Plan-Apochromat-63x-1.4-Oil-DIC-M27|420782-9900-799]]  |
+|  <fc #2c80c0>63x</fc>  |  Plan-Apochromat DIC  |  Oil  |  1.40  |  0.19  |  [[https://www.micro-shop.zeiss.com/en/de/shop/objectives/420782-9900-799/Objective-Plan-Apochromat-63x-1.4-Oil-DIC-M27|420782-9900-799]]  |
-*ask staff for help setting up the proper immersion medium setting
+* please ask staff for help setting up the proper immersion medium setting
+==== Airyscan 2 emission filters =====
-==== Detector(s) ====
-x blue-green multialkali PMT (15-20% QE)
-x GaAsP PMT spectral detectors (tunable between 450-750 nm) (~45% QE)
-x green-red multialkali PMT  (10-45% QE)
-x T-PMT detector (brighfield)
-x Airyscan2 detector (45% QE after processing Airyscan data)
-==== Airyscan2 emission filters =====
 ^  Position  ^  Emission  ^
-|  1  |    |
+|  1  |  Plate  |
-|  2  |    |
+|  2  |  <fc #0046ff>BP 420 - 480</fc> + <fc #00ff92>BP 495 - 550</fc>  |
-|  3  |    |
+|  3  |  <fc #0028ff>BP 420 - 470</fc> + <fc #ffbe00>BP 570 - 630</fc>  |
-|  4  |    |
+|  4  |  <fc #007bff>BP 420 - 500</fc> + <fc #ffad00>LP 605</fc>  |
-|  5  |    |
+|  5  |  <fc #00eaff>BP 465 - 505</fc> + <fc #b3ff00>BP 525 - 585</fc>  |
-|  6  |    |
+|  6  |  <fc #1fff00>BP 495 - 550</fc> + <fc #ffbe00>BP 570 - 630</fc>  |
-|  7  |    |
+|  7  |  <fc #4aff00>BP 495 - 555</fc> + <fc #ff0000>LP 660</fc>  |
-|  8  |    |
+|  8  |  <fc #ffcf00>BP 570 - 620</fc> + <fc #ff0000>LP 660</fc>  |
-==== Eyepiece filterset(s) (COLIBRI LED illumination) =====
+==== Detectors ====
-^  Position  ^  Transmission  ^  Description (use)  ^  Excitation   ^
-|  DAPI  |  445/50 nm  |  <fc #00ffff>DAPI, CFP or Hoechst filter</fc>  |  385nm   |
-|  GFP   |  525/50 nm  |  <fc #00ff00>RFP or TRITC (LongPass)</fc>  |   493nm  |
-|  RFP   |  LP590 nm  |  <fc #ffa500>GFP or FITC filter</fc>  |  555nm  |
-|  Mirror   |  -  |  Mirror for LSM  |  -  |
+  * 1x blue-green multialkali PMT (15-20% QE)
+  * 4x GaAsP PMT spectral detectors (tunable between 450-750 nm) (~45% QE)
+  * 1x green-red multialkali PMT  (10-25% QE)
+  * 1x T-PMT detector (brighfield)
+  * 1x Airyscan2 detector (~45% QE after processing Airyscan data)
-===== Turning ON =====
-. Verify if the fluorescent lamp is not hot (touch it), otherwise wait until it’s cold (10-15min). Afterwards, turn on the switch. NOTE. If Zen or the microscope are started with the fluorescence illuminator "OFF" they will not see it and need to be restarted afterwards.
+===== How to start your session =====
-. Turn on the microscope and the Definite focus control box.
+If you are the **first user** of the day:
-. Turn on laser key (turn laser key clockwise (or counter-clockwise?) to downward position) in the unit below the table.
+  * Turn off Main Switch
+{{::O_LSM980_MS.png?100|}}
+  * Turn on the computer
+  * Turn on HXP, and incubation module (if needed)
+{{::Oeiras_LSM980_hxp.png?129|}}
+{{::Oeiras_LSM980_incubation.png?100|}}
+  * Turn on Main Switch
+  * Log in to Windows with your Agendo credentials
+  * Start **ZEN**
-. Login into your aGina account on the computer. Start ZEN Blue 3.3.
+Else:
+  * Log in to Windows with your Agendo credentials
+  * Start **ZEN**
-===== Turning OFF =====
+===== How to end your session =====
-DO NOT TURN OFF THE COMPONENTS SWITCH, AND THE STAGE AND PIEZO CONTROLLERS (UNDER THE TABLE)
+If there is another user:
+  * Clean up immersion objectives
+  * Exit the ZEN software
+  * Log off the computer
+  * Turn off HXP, and incubation module (if > 1 hour for the next user)
+If you are the **last user** of the day:
+  * Clean up immersion objectives
+  * Exit the ZEN software
+  * Turn off the computer
+  * Turn off HXP, and incubation module (if used)
-. Remove the sample and Gently wipe with optic cleaning paper and EtOH paper the immersion objective(s) used. If you suspect the objective needs deep cleaning please inform the staff.
-. Transfer your data to the institutional server (never connect USB sticks or disks on this workstation).
-. Check that the incubator(s) are off, unless they are needed by the next user (ask staff).
-. Close ZEN and logout from windows (if there’s an user after you, you can now leave the microscope).
-If there is no one in the next 2h, turn off the fluorescence lamp (behind the computer screen) and also exit Zen.
-If you are the last user of the day (check bookings in Agendo): Turn off Laser key (to horizontal position) in the large unit under the table and turn off the microscope and definite focus control box.
 ----
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