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Zeiss Axioscan Z1 Slide scanner

Desmarais Building, Room 5308-2
Simple Microscope usage price

Instrument kindly provided to the CI2B by – in 2025

  • Slide scanner
  • Transmitted light
  • Brightfield color and monochrome
  • Pseudo-Phase contrast
  • Fluorescence for dyes like DAPI, FITC, DsRed, Cy5 and Cy7



Light sources

  • LED lamp for transmitted light
  • Viluma 7 FR-R[G/Y]BV-UV for fluorescence

Channel

Emission peak (nm)

Nominal Power (mW)Measured Power (mW)
Compatible Dyes
UV385/30
 DAPI, Hoechst 33342, Hoechst 33258, Alexa Fluor 350, Alexa Fluor 405, Indo-1, eBFP / BFP, eGFP (wt), True Blue
V423/44
 Pacific Blue, Lucifer Yellow, Alexa Fluor 433, eCFP, Cerulean
B469/38
 

FM1-43, Cy2, eGFP, NBD, MitoTracker Green, Alexa Fluor 488, Fluo-4, BCECF, Calcein, DiO SNAFL, YO-Pro-1, Nissl, LysoSensor Green, mHoneydew, FITC / Fluorescein, Kaede (green / red), PerCP, YoYo-1, FuraRed

G555/30
 TRITC, 7-AAD, Cy3, tdTomato, Alexa Fluor 546, Alexa Fluor 555, DsRed, mOrange, TagRFP, SNARF, DyLight 549, Spectrum Orange
Y591/27
 MitoTracker RED FM/CMXRos, txRed, mCherry, mRFP1, Cy3.5, Rhodamine B, Alexa Fluor 568, Dylight 594, Alexa Fluor 594, Bodipy TR
R631/33
 Alexa Fluor 633, Alexa Fluor 647, Cy5, DRAQ5, ToTo-3, ATTO-655, MitoTracker DeepRed, APC, ATTO-647N
FR735/40
 Alexa Fluor 750, Alexa Fluor 790, Cy7, Cy7.5

Total output 1510 mW

The information above does not directly indicate the effective intensity provided by the instrument as Zeiss does not provide the nominal power of their light sources,excepted the total output being 1510 mW. The graph on the left only indicates the emission filter bandwidth while the graph on the right compared the normalized relative intensities between the Viluma and the historic HXP 120 mercury bulb lightsource.  Finally both graphs are misleading since they present 8 individual channels which can't be provided within the same product. The Viluma 7 can only provide 7 individual channel. In this case, the model included in this instrument does not have the Cyan Channel.
Zeiss_Viluma_Product Info.pdf

Objectives

  • 5x/0.25 Air 420130-9900-000
  • 10x/0.45 Air 420640-9900-000
  • 20x/0.8 Air 420650-9903-000
  • 40x/0.95 Air 420660-997

Dichroic

  • FilterSet 112 405/495/575/654/761 489112-8016-000

Emission filters

  1. Empty
  2. BP 425/30 412-438 489090-8001-000
  3. BP 514/30 501-527 489090-8002-000
  4. BP 592/25 583-601 489090-8003-000
  5. BP 681/45 662-700 489112-8001-000
  6. BP 788/38 770-800 489112-8002-000

Detectors

  • Zeiss AxioCam 705 Color
CameraZeiss AxioCam 705 Color

Sensor Type

CMOS

Sensor Category

Color

Nb Pixels

 5.07 M

Pixel Layout

2464 × 2056 

Pixel size

 3.45 µm × 3.45 µm

Sensor size

 8.5 mm x  7.1 mm

Sensor diameter

 11.1 mm

Bit depth

14-bit
Speed at full resolution60 images/s

Max QE

 80 % @ 540nm
Readout noise2.2 e⁻

Cooling

18C Thermoelectric

Dark Current

 0.5 e⁻/pixel/sec

Full well capacity

11 000 e-

Dynamic Range

1:5000
1: 25 000 HDR mode

Interface

USB B 3.0

Mount

C-mount

  • Hamamatsu ORCA-Flash4.0 V3
CameraHamamatsu ORCA-Flash4.0 V3

Sensor Type

sCMOS

Sensor Category

Monochrome

Nb Pixels

4.2 M

Pixel Layout

2048 x 2048

Pixel size

  6.5 um

Sensor size

13.312 mm x 13.312 mm

Sensor diameter

18.826 mm

Bit depth

16-bit
Speed at full resolution30 images/s

Max QE

82 % at 560 nm
Reading noise0.8 e⁻

Cooling

Air cooled -10C

Dark Current

0.06 e⁻/pixel/sec

Full well capacity

30 000 e-

Dynamic Range

1:37000

Interface

USB 3.0 or Camera-Link

Mount

C-mount


  • If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
  • Turn on the instrument power bar (#2) on the desk between the instrument and the computer
  • Turn on the instrument (#3) on the left side of the instrument
  • Start Zen

This instrument is only offered with service. Please contact us.


  • Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
  • At the end of each session, copy your data to your external drive and delete it from the local C: drive
  • You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).

In any case, your files should be removed from the C: drive.

  • Save your data
  • Close Zen
  • Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  • Turn off the microscope power bar (#1)
  • Turn off the computer

Reminder

  • Take back your samples including ones in the microscope
  • Leave the microscope and the working area clean

  • Added to the Wiki
  • Connected to Processing workstation with 10 GB cable
  • Purchase and Installation

Stand

Zeiss AxioScan  Z1 Serial:
System ID: 4661000608

Light sources

  • Transmitted LED light
  • Viluma 7 FR-R[G/Y]BV-UV  Model 423052-9771-000

Objectives

  • 5x/0.25 Air 420130-9900-000
  • 10x/0.45 Air 420640-9900-000
  • 20x/0.8 Air 420650-9903-000
  • 40x/0.95 Air 420660-9970-000
  • Empty
  • Empty
  • Empty

Stage

  • 25x Motorized Loader
  • 10x Inserts 10 x 4 slide 25x75
  • 10x Inserts 10 x 2 slide 50x75

Filters

  • Beam splitter
    1. Empty
    2. Filter Set 112 PBS 405 - 495 - 575 - 654 - 761 489112-8016-000
    3. Empty
    4. Empty
    5. Empty
    6. Empty
  • Emission Filter
    1. Empty
    2. DAPI BP 425/30 412-438 489090-8001-000
    3. FITC BP 514/30 501-527 489090-8002-000
    4. DsRed BP 592/25 583-601 489090-8003-000
    5. Cy5 BP 681/45 662-700 489112-8001-000
    6. Cy7 BP 788/38 770-800 489112-8002-000

Detector

  • Zeiss AxioCam 705 color Serial: 
  • Hamamatsu ORCA Flash4.0 V3
  • Zeiss AxioCam 105 R2 (preview)

Workstation

  • HP Z8 Fury G5  Serial 
  • I155441-CIB
  • Intel Xeon w7-3455 @ 2.5 GHz
  • Motherboard HP 88C1 Chipset Intel W790
  • BIOS U61 2024-07-11
  • RAM 128 GB (4 x 32 GB) DDR5 2400 MHz
  • OS NVMe Western Digital SN850X 2 TB 6000 MB/s
  • OS Windows 11 24H2
  • SWAP Drive NVMe Physon PSEIN004TA87MC0 4 TB 6500 MB/s
  • Data Storage 10 TB HD Data Storage (2 x 12 TB RAID 0 Western Digital UltraStar HGST HUH721212ALE604) 160 MB/s
  • Video Card nVidia RTX A2000 12 GB GDDR6
  • Monitor HP 738pu HPN3A12 Native resolution 3840 x 1600
  • Software Zen Blue 3.11

Manuals

Troubleshooting

Technical support is free and unlimited. Contact us !

FAQ

No. This is a slide scanner dedicated to digitize size mounted between a slide and a 0.17mm thick coverslip.

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Content published under CC BY-SA 4.0. Sharing allowed under the same license with attribution: "Original content by l'Institut Courtois d'innovation biomédicale, used under CC BY-SA 4.0"

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