agilent_cytation_5
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agilent_cytation_5 [2025/01/08 16:11] bioimaging [Microscope Turn On Procedure] |
agilent_cytation_5 [2025/12/12 10:56] (current) bioimaging |
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| <a href="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg" width=300></a> | <a href="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg"><img src="/facility/bioimaging/lib/exe/fetch.php?media=cytation.jpg" 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>: [Oeiras] Room 0B16<br> | + | <b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=bartolomeu_dias_wing_2025_-_cytation_5.png">[Oeiras] Room 0B16</a><br> |
| <b>Manufacturer</b>: <a href="https://www.agilent.com/" target="_blank">Agilent</a> <br> | <b>Manufacturer</b>: <a href="https://www.agilent.com/" target="_blank">Agilent</a> <br> | ||
| <b>Model</b>: <a href="https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-multimode-readers/biotek-cytation-5-cell-imaging-multimode-reader-1623202" target="_blank">BioTek Cytation 5 Cell Imaging Multimode Reader</a> <br> | <b>Model</b>: <a href="https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-multimode-readers/biotek-cytation-5-cell-imaging-multimode-reader-1623202" target="_blank">BioTek Cytation 5 Cell Imaging Multimode Reader</a> <br> | ||
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| <b>Software</b>: Gen 5 Image Prime <br> | <b>Software</b>: Gen 5 Image Prime <br> | ||
| <b>Year</b>: 2024 <br> | <b>Year</b>: 2024 <br> | ||
| - | <b>SN</b>: <br> | + | <b>SN</b>: 2302240B<br> |
|   <br> |   <br> | ||
| Data will be deleted after: <b>1 month</b> | Data will be deleted after: <b>1 month</b> | ||
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| It is also equipped with an atmosphere control unit for regulating CO2 concentration (for live cell imaging), and capable of setting up for hypoxia conditions also. The multimode detection modules include filter- and monochromator-based fluorescence detection, luminescence, and UV-Vis absorbance detection. | It is also equipped with an atmosphere control unit for regulating CO2 concentration (for live cell imaging), and capable of setting up for hypoxia conditions also. The multimode detection modules include filter- and monochromator-based fluorescence detection, luminescence, and UV-Vis absorbance detection. | ||
| + | ===== System Components ===== | ||
| - | ===== Filtersets available ===== | + | ==== LEDs ==== |
| - | ^ Default Config ^ Filterset ^ Filterset Reference ^ LED wavelength (nm) ^ LED reference ^ Excitation (nm) ^ Dichroic (nm) ^ Emission (nm) ^ Default Config ^ | + | ^ Line ^ Wavelength ^ Reference ^ |
| - | | Pos 1 | Laser Autofocus | [[https://www.agilent.com/store/productDetail.jsp?catalogId=1225010&catId=SubCat2ECS_2041516|1225010]] | - | - | - | - | - | | + | | UV | <fc #be00cc>385 nm</fc> | 1225007 | |
| - | | Pos 2 | DAPI | [[https://www.agilent.com/store/en_US/Prod-1225100/1225100|1225100]] | 365 | 1225007 | 377/50 | 409 | 447/60 | | + | | B | <fc #0092ff>465 nm</fc> | 1225001 | |
| - | | - | GFP | [[https://www.agilent.com/store/en_US/Prod-1225101/1225101|1225101]] | 465 | 1225001 | 469/35 | 497 | 525/39 | | + | | G | <fc #42ff00>523 nm</fc> | 1225003 | |
| - | | Pos 3 | Propidium Iodide | [[https://www.agilent.com/store/en_US/Prod-1225111/1225111|1225111]] | 523 | 1225003 | 531/40 | 605 | 647/57 | | + | | Y | <fc #ffdf00>590 nm</fc> | 1225002 | |
| - | | - | Texas Red | [[https://www.agilent.com/store/en_US/Prod-1225102/1225102|1225102]] | 590 | 1225002 | 586/15 | 605 | 647/57 | | + | | R | <fc #ff6b00>623 nm</fc> | 1225005 | |
| - | | Pos 4 | Cy5 | [[https://www.agilent.com/store/en_US/Prod-1225105/|1225105]] | 623 | 1225005 | 628/40 | 660 | 685/40 | | + | |
| + | ==== Filtersets available ==== | ||
| + | |||
| + | ^ Position ^ Filterset ^ Excitation ^ Dichroic ^ Emission ^ Reference ^ | ||
| + | | 1 | LASER Autofocus | - | - | - | [[https://www.agilent.com/store/productDetail.jsp?catalogId=1225010&catId=SubCat2ECS_2041516|1225010]] | | ||
| + | | 2 | DAPI | 352-402 nm | 409 nm | <fc #0035ff>417-477 nm</fc> | [[https://www.agilent.com/store/en_US/Prod-1225100/1225100|1225100]] | | ||
| + | | - | GFP | 453-488 nm | 497 nm | <fc #4aff00>505-545 nm</fc> |[[https://www.agilent.com/store/en_US/Prod-1225101/1225101|1225101]] | | ||
| + | | 3 | Propidium Iodide | 511-551 nm | 605 nm | <fc #ff0000>619-676 nm</fc> |[[https://www.agilent.com/store/en_US/Prod-1225111/1225111|1225111]] | | ||
| + | | - | Texas Red | 579-594 nm | 605 nm | <fc #ff0000>619-676 nm</fc> | [[https://www.agilent.com/store/en_US/Prod-1225102/1225102|1225102]] | | ||
| + | | 4 | Cy5 | 608-648 nm | 660 nm | <fc #ff0000>665-705 nm</fc> | [[https://www.agilent.com/store/en_US/Prod-1225105/|1225105]] | | ||
| + | |||
| + | ==== Objectives ==== | ||
| - | ===== Objectives ===== | ||
| ^ Magnification ^ Model ^ Immersion ^ NA ^ WD (mm) ^ Reference ^ | ^ Magnification ^ Model ^ Immersion ^ NA ^ WD (mm) ^ Reference ^ | ||
| | 4x | Plan-Semiapochromat Fluorescence | Air | 0.13 | 17 | [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706528|UPLFLN4X]] | | | 4x | Plan-Semiapochromat Fluorescence | Air | 0.13 | 17 | [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706528|UPLFLN4X]] | | ||
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| | 40x | Plan-Semiapochromat Fluorescence | Air | 0.6 | 2.70-4.00 | [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706551|LUCPLFLN40X]] | | | 40x | Plan-Semiapochromat Fluorescence | Air | 0.6 | 2.70-4.00 | [[https://www.olympus-lifescience.com/en/objective-finder/#!objective=511706551|LUCPLFLN40X]] | | ||
| - | + | ==== Camera ==== | |
| - | ===== Camera ===== | + | |
| ^ Model ^ Frame Size ^ Pixel Size (µm) ^ Quantum Efficiency ^ | ^ Model ^ Frame Size ^ Pixel Size (µm) ^ Quantum Efficiency ^ | ||
| | [[https://www.teledynevisionsolutions.com/products/chameleon3-usb3/?model=CM3-U3-50S5M-CS&vertical=machine%20vision&segment=iis|FLIR Chameleon3 CM3-U3-50S5M (mono)]] | 2448 × 2048 | 3.45 x 3.45 | 69% (at 525 nm) | | | [[https://www.teledynevisionsolutions.com/products/chameleon3-usb3/?model=CM3-U3-50S5M-CS&vertical=machine%20vision&segment=iis|FLIR Chameleon3 CM3-U3-50S5M (mono)]] | 2448 × 2048 | 3.45 x 3.45 | 69% (at 525 nm) | | ||
| + | ==== Pixel Size ==== | ||
| - | ===== CO2/O2 Control Procedure ===== | + | Images coming from the Cytation 5 are not calibrated, even though the system has that information available. In the images' metadata you can find the PixelWidth and the ImageWidthMicrons, and by dividing the latter for the first, you get the Pixel Size to calibrate your images. |
| + | You can find this information below, per objective and Field Of View (FOV): | ||
| - | * **If you require CO2/O2 control**, turn the **atmosphere controller ON**. | + | ^ Objective ^ FOV ^ Image Size (pixels) ^ Image Size (microns) ^ Pixel Size (microns) ^ |
| - | {{cytation_gas_1.png?|}} | + | | 4x | Full | 1992 x 1992 | 3474 x 3474 | ~1.7440 x ~1.7440 | |
| - | * Confirm the **CO2/O2 switch is ON**, and set to the desired percentage. | + | | 4x | 75% | 1496 x 1496 | 2609 x 2609 | ~1.7440 x ~1.7440 | |
| - | {{cytation_gas_2.png?|}} | + | | 4x | Standard | 1224 x 904 | 2135 x 1576 | ~1.7443 x ~1.7434 | |
| - | * **Open the CO2/N2 tap** on the wall. | + | | 20x | Full | 1992 x 1992 | 694 x 694 | ~0.3484 x ~0.3484 | |
| - | {{cytation_gas_3.png?|}} | + | | 20x | 75% | 1496 x 1496 | 521 x 521 | ~0.3483 x ~0.3483 | |
| + | | 20x | Standard | 1224 x 904 | 427 x 315 | ~0.3489 x ~0.3485 | | ||
| + | | 40x | Full | 1992 x 1992 | 347 x 347 | ~0.1742 x ~0.1742 | | ||
| + | | 40x | 75% | 1496 x 1496 | 260 x 260 | ~0.1738 x ~0.1738 | | ||
| + | | 40x | Standard | 1224 x 904 | 213 x 157 | ~0.1740 x ~0.1737 | | ||
| + | ===== CO2 and/or O2 Control Procedure ===== | ||
| + | |||
| + | * **If you require CO2 and/or O2 control**, turn the **atmosphere controller ON**. | ||
| + | {{cytation_gas_1.png?200|}} | ||
| + | * Confirm the **CO2 and/or O2 switch is ON**, and set to the desired percentage. | ||
| + | {{cytation_gas_2.png?600|}} | ||
| + | * **Open the CO2 and/or N2 tap** on the wall. | ||
| + | {{cytation_gas_3.png?200|}} | ||
| ===== Microscope Turn On Procedure ===== | ===== Microscope Turn On Procedure ===== | ||
| * Turn on the microscope using the **switch** at the **front of the system**. | * Turn on the microscope using the **switch** at the **front of the system**. | ||
| - | {{cytation_turnon_1.png?|}} | + | {{cytation_turnon_1.png?200|}} |
| - | * Turn the **computer** on. | + | * Turn the **computer** on (if needed). |
| - | {{cytation_turnon_2.png?|}} | + | {{cytation_turnon_2.png?200|}} |
| * **Login** to Windows with your **GIMM Agendo credentials**. | * **Login** to Windows with your **GIMM Agendo credentials**. | ||
| * Wait for the **button light** in the front to **turn green** (the system will pop out the plate drawer as well). | * Wait for the **button light** in the front to **turn green** (the system will pop out the plate drawer as well). | ||
| - | {{cytation_turnon_3.png?|}} | + | {{cytation_turnon_3.png?200|}} |
| * Open the **Gen 5** software. | * Open the **Gen 5** software. | ||
| - | |||
| ===== Microscope Turn Off Procedure ===== | ===== Microscope Turn Off Procedure ===== | ||
| * Turn off the microscope using the **switch** at the **front of the system**. | * Turn off the microscope using the **switch** at the **front of the system**. | ||
| - | {{cytation_turnon_1.png?|}} | + | {{cytation_turnon_1.png?200|}} |
| - | * **Sign out** of the computer. | + | * **Log off** the computer. |
| - | * If you used the gas controller, **Turn it OFF** and **close all wall taps**. | + | * **If you used the gas controller** |
| - | {{cytation_gas_1.png?|}} | + | * Turn gas controller OFF |
| - | {{cytation_gas_3.png?|}} | + | {{cytation_gas_1.png?200|}} |
| + | * Close all wall taps. | ||
| + | {{cytation_gas_3.png?200|}} | ||
| ---- | ---- | ||
| [[resources|Back to the Equipment page]] | [[resources|Back to the Equipment page]] | ||
agilent_cytation_5.1736349072.txt.gz · Last modified: 2025/01/08 16:11 by bioimaging
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