# Zeiss Axioscan 7

#### Location: HCI Room 1470

[![CI-Axio7.jpg](https://bookstack.cores.utah.edu/uploads/images/gallery/2024-03/scaled-1680-/ci-axio7.jpg)](https://bookstack.cores.utah.edu/uploads/images/gallery/2024-03/ci-axio7.jpg)

The Zeiss AxioScan 7 is a fast and flexible slide scanner that digitizes specimens to produce high-quality virtual slides. In addition to brightfield slide scanning, the Axioscan 7 can scan up to five fluorescent channels using fast switching LED lights. Up to 100 slides can be loaded onto the scanner, making it suitable for large projects, including digital archives. Scanned images are saved as CZI files and can be viewed using Zeiss freeware Zen-lite or third-party image analysis programs.

#### Main Features of the Axioscan 7:

- Holds up to 100 slides.
- Able to image both bright-field (e.g. H&E slides) and up to nine-colour fluorescent samples.
- Image areas can be detected automatically or marked out, to form montages of the whole sample, or multiple samples on each slide
- Setup wizard to guide users through optimising image acquisition and autofocus parameters.
- Once setup, the system can be left for unattended automated scanning e.g. overnight

#### Suggested Applications:

- Fixed slides.

#### Configurations:

The Axioscan 7 has a replaceable filter turret and can be switched between two light sources. The 10 position filter cube turret is typically used with the Colibri 7 switchable LED source. The fast filter wheel is typically used with the X-Cite Xylis LED source.

<table border="1" class="align-left" id="bkmrk-configuration-light-" style="border-collapse: collapse; width: 100%;"><colgroup><col style="width: 33.333333%;"></col><col style="width: 33.333333%;"></col><col style="width: 33.333333%;"></col></colgroup><tbody><tr><td class="align-left">**Configuration**</td><td class="align-left">**Light Source**</td><td class="align-left">**Filter Set**</td></tr><tr><td class="align-left">1</td><td>Colibri 7</td><td>Filter Cubes</td></tr><tr><td class="align-left">2</td><td>X-Cite Xylis</td><td>Fast Filter Wheel</td></tr></tbody></table>

Only Cell Imaging staff are permitted to switch between configurations. Please schedule our time and plan accordingly.

 <span style="color: rgb(34, 34, 34); font-family: var(--font-heading, var(--font-body)); font-size: 1.666em;">Light Sources:</span>

##### Colibri 7:

The Colibri 7 has 6 LEDs with excitation filters to provide 7 excitation bands. (One LED has a motorized filter to split it into two bands.)

Excitation Bands <span style="background-color: rgb(224, 62, 45);">(There is one too many here)</span>

<table border="1" id="bkmrk-band-wavelength-%2F-ba" style="border-collapse: collapse; width: 100%; height: 261px;"><colgroup><col style="width: 11.111111%;"></col><col style="width: 25.185185%;"></col><col style="width: 63.580247%;"></col></colgroup><tbody><tr style="height: 29px;"><td style="height: 29px;">Band</td><td style="height: 29px;">Wavelength / Bandwidth (nm)</td><td style="height: 29px;">Some typical fluorophores</td></tr><tr style="height: 29px;"><td style="height: 29px;">UV</td><td style="height: 29px;">385/30</td><td style="height: 29px;">API, Hoechst 33342, Hoechst 33258, Alexa Fluor 350, Alexa Fluor 405, Indo-1, eBFP / BFP, eGFP (wt), True Blue

</td></tr><tr style="height: 29px;"><td style="height: 29px;">V</td><td style="height: 29px;">423/44</td><td style="height: 29px;">Pacific Blue, Lucifer Yellow, Alexa Fluor 433, eCFP, Cerulean

</td></tr><tr style="height: 29px;"><td style="height: 29px;">B</td><td style="height: 29px;">469/38</td><td style="height: 29px;">FM1-43, Cy2, eGFP, NBD, MitoTracker Green, Alexa Fluor 488, BCECF, Calcein, DiO SNAFL, YO-Pro-1, Nissl, LysoSensor Green, mHoneydew, FITC / Fluorescein, Kaede (green / red), PerCP, YoYo-1,FuraRed

</td></tr><tr style="height: 29px;"><td style="height: 29px;">C</td><td style="height: 29px;">511/44</td><td style="height: 29px;">Rhodamine 123, Fluo-4, Oregon Green BAPTA, Sytox Green, eYFP, FM4-64, Eosin/HE, Acridine Orange, JC1, Bodipy FL, Propidium Iodide, Spectrum Green, Calcium Green

</td></tr><tr style="height: 29px;"><td style="height: 29px;">G</td><td style="height: 29px;">555/30</td><td style="height: 29px;">TRITC, 7-AAD, Cy3, tdTomato, Alexa Fluor 546, Alexa Fluor 555, DsRed, mOrange, TagRFP, SNARF, DyLight 549, Spectrum Orange

</td></tr><tr style="height: 29px;"><td style="height: 29px;">Y</td><td style="height: 29px;">590/27</td><td style="height: 29px;">MitoTracker RED FM/CMXRos, txRed, mCherry, mRFP1, Cy3.5, Rhodamine B, Alexa Fluor 568, Dylight 594, Alexa Fluor 594, Bodipy TR

</td></tr><tr style="height: 29px;"><td style="height: 29px;">R</td><td style="height: 29px;">631/33</td><td style="height: 29px;">Alexa Fluor 633, Alexa Fluor 647, Cy5, DRAQ5, ToTo-3, ATTO-655, MitoTracker DeepRed, APC, ATTO-647N

</td></tr><tr style="height: 29px;"><td style="height: 29px;">FR</td><td style="height: 29px;">735/40</td><td style="height: 29px;">Alexa Fluor 750, Alexa Fluor 790, Cy7, Cy7.5

</td></tr></tbody></table>

##### X-Cite Xylis:

The X-Cite Xylis XT720L is a broad spectrum illuminator with a range from 380-770nm. It has peaks at 385, 430, 475, 545, 635, 735nm.

#### Filters:

##### Filter Cubes:

In multi-band fluorescence imaging, the filter turret has to move between positions for each band. This is usually done on a per-tile basis. At about 400ms per move, this can add up, especially for a large scan at higher magnification. The Axioscan 7 has 2 multi-band cubes. If these can be used, it can reduce or eliminate these moves and reduce scan time. These can be used on the Axioscan 7 because it has the Colibri 7 switching LED source.

<table border="1" cellpadding="0" cellspacing="0" class="MsoNormalTable" id="bkmrk-filter-no-%C2%A0fluorochr" style="height: 549px; border-collapse: collapse; width: 790px; border-width: 1px; border-spacing: 0px;" width="483"><tbody><tr style="height: 79px;"><td style="height: 79px; border-width: 1px; width: 65.59375px;">**Filter No**

</td><td style="height: 79px; border-width: 1px; width: 203.75px;"> **Fluorochrome**

</td><td style="height: 79px; border-width: 1px; width: 122.71875px;">**Excitation (nm)**

</td><td style="height: 79px; border-width: 1px; width: 125.046875px;">**Beamsplitter (nm)**

</td><td style="height: 79px; border-width: 1px; width: 272.8125px;">**Emission (nm)**

</td></tr><tr style="height: 35px;"><td style="height: 35px; border-width: 1px; width: 65.59375px;">1

</td><td style="height: 35px; border-width: 1px; width: 203.75px;">Empty (Brightfield)

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 122.71875px;"></td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 125.046875px;"></td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 272.8125px;"></td></tr><tr style="height: 35px;"><td style="height: 35px; border-width: 1px; width: 65.59375px;">2

</td><td style="height: 35px; border-width: 1px; width: 203.75px;">HE GFP

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 122.71875px;">450-490

</td><td style="height: 35px; border-width: 1px; width: 125.046875px;">495

</td><td style="height: 35px; border-width: 1px; width: 272.8125px;">500-550

</td></tr><tr style="height: 35px;"><td style="height: 35px; border-width: 1px; width: 65.59375px;">3

</td><td style="height: 35px; border-width: 1px; width: 203.75px;">HE DsRed

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 122.71875px;">538-562

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 125.046875px;">570

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 272.8125px;">570-640

</td></tr><tr style="height: 35px;"><td style="height: 35px; border-width: 1px; width: 65.59375px;">4

</td><td style="height: 35px; border-width: 1px; width: 203.75px;">Cy5

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 122.71875px;">625-655

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 125.046875px;">660

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 272.8125px;">665-715

</td></tr><tr style="height: 35px;"><td style="height: 35px; border-width: 1px; width: 65.59375px;">5

</td><td style="height: 35px; border-width: 1px; width: 203.75px;">HE BFP

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 122.71875px;">370-410

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 125.046875px;">420

</td><td nowrap="nowrap" style="height: 35px; border-width: 1px; width: 272.8125px;">430-470

</td></tr><tr style="height: 101px;"><td style="height: 101px; border-width: 1px; width: 65.59375px;">6

</td><td style="height: 101px; border-width: 1px; width: 203.75px;">HE DAPI/GFP/Cy3.5/Cy7

</td><td nowrap="nowrap" style="height: 101px; border-width: 1px; width: 122.71875px;">375-395

455-483

583-600

720-750

</td><td nowrap="nowrap" style="height: 101px; border-width: 1px; width: 125.046875px;">405

493

611

762

</td><td nowrap="nowrap" style="height: 101px; border-width: 1px; width: 272.8125px;">410-440

501-547

618-650

770-800

</td></tr><tr style="height: 123px;"><td style="height: 123px; border-width: 1px; width: 65.59375px;">7

</td><td style="height: 123px; border-width: 1px; width: 203.75px;">HE DAPI/GFP/Cy3.5/Cy5/Cy7

</td><td nowrap="nowrap" style="height: 123px; border-width: 1px; width: 122.71875px;">370-400

450-488

540-570

614-647

720-750

</td><td nowrap="nowrap" style="height: 123px; border-width: 1px; width: 125.046875px;">405

493

575

654

761

</td><td nowrap="nowrap" style="height: 123px; border-width: 1px; width: 272.8125px;">412-438

501-527

582-601

662-700

770-800

</td></tr><tr><td style="border-width: 1px; width: 65.59375px;">Pol

</td><td style="border-width: 1px; width: 203.75px;">Circular polarizer and analyzer

</td><td style="border-width: 1px; width: 122.71875px;"></td><td style="border-width: 1px; width: 125.046875px;"></td><td style="border-width: 1px; width: 272.8125px;"></td></tr><tr><td style="border-width: 1px; width: 65.59375px;">ND

</td><td style="border-width: 1px; width: 203.75px;">6% Neutral Density Filter

</td><td style="border-width: 1px; width: 122.71875px;"></td><td style="border-width: 1px; width: 125.046875px;"></td><td style="border-width: 1px; width: 272.8125px;"></td></tr></tbody></table>

##### Fast Filter Wheel:

The fast filter wheel moves between filter positions about 10 times faster than the filter cube turret.

<span style="background-color: rgb(224, 62, 45);">Need information here</span>

<table border="1" id="bkmrk-filter-pass-peak-and" style="border-collapse: collapse; width: 100%;"><colgroup><col style="width: 33.333333%;"></col><col style="width: 33.333333%;"></col><col style="width: 33.333333%;"></col></colgroup><tbody><tr><td>Filter</td><td>Pass Peak and Width</td><td>Typical fluorophores</td></tr><tr><td>Empty (Brightfield)</td><td>  
</td><td>  
</td></tr><tr><td>Single Channel 1</td><td>  
</td><td>  
</td></tr><tr><td>Single Channel 2</td><td>  
</td><td>  
</td></tr><tr><td>Single Channel 3</td><td>  
</td><td>  
</td></tr><tr><td>Dual Channel 4</td><td>  
</td><td>  
</td></tr><tr><td>Dual Channel 5</td><td>  
</td><td>  
</td></tr></tbody></table>

#### Objectives:

<table border="1" id="bkmrk-magnification-immers" style="width: 100%;"><tbody><tr><td style="width: 18.4178%;">**Objective**</td><td style="width: 14.21508%;">**Magnification**</td><td style="width: 11.495674%;">**Immersion**</td><td style="width: 12.23733%;">**Numerical**

**Apperature**

</td><td style="width: 12.608158%;">**Correction Ring**</td><td style="width: 13.226205%;">**Coverglass (mm)**</td><td style="width: 17.799753%;">**Working**

**Distance (mm)**

</td></tr><tr><td style="width: 18.4178%;">Fluar M27</td><td style="width: 14.21508%;">5X</td><td style="width: 11.495674%;">Air</td><td style="width: 12.23733%;">0.25</td><td style="width: 12.608158%;">  
</td><td style="width: 13.226205%;">0.17</td><td style="width: 17.799753%;">12.5

</td></tr><tr><td style="width: 18.4178%;">Pan Apo M27</td><td style="width: 14.21508%;">10X</td><td style="width: 11.495674%;">Air</td><td style="width: 12.23733%;">0.45</td><td style="width: 12.608158%;">  
</td><td style="width: 13.226205%;">0.17</td><td style="width: 17.799753%;">2.1</td></tr><tr><td style="width: 18.4178%;">Pan Apo M27</td><td style="width: 14.21508%;">20X</td><td style="width: 11.495674%;">Air</td><td style="width: 12.23733%;">0.8</td><td style="width: 12.608158%;">  
</td><td style="width: 13.226205%;">0.17</td><td style="width: 17.799753%;">0.55</td></tr><tr><td style="width: 18.4178%;">Pan Apo Korr M27</td><td style="width: 14.21508%;">40X</td><td style="width: 11.495674%;">Air</td><td style="width: 12.23733%;">0.95</td><td style="width: 12.608158%;">  
</td><td style="width: 13.226205%;">0.13-0.21</td><td style="width: 17.799753%;">0.25</td></tr><tr><td style="width: 18.4178%;">EC Pan-Neofluar Pol M27</td><td style="width: 14.21508%;">20X</td><td style="width: 11.495674%;">Air</td><td style="width: 12.23733%;">0.5</td><td style="width: 12.608158%;">  
</td><td style="width: 13.226205%;">0.17</td><td style="width: 17.799753%;">2</td></tr></tbody></table>