To integrate the Zeiss Axio Observer 7 or .Z1 with the CODEX instrument and run CODEX experiments, the following minimum hardware and software requirements need to be met. Consult with your Zeiss representative for the final design and the most up-to-date components.


CODEX system requires ZEN Blue 2.3, 2.5, or 2.6.

The following software modules are required for CODEX :

  • ZEN Module Z Stack (PN 410136-1030-110)

  • ZEN Module Tiles (PN 410136-1025-110)

  • ZEN Module Autofocus (PN 410136-1028-110)



Zeiss Axio Observer 7 / .Z1


• Scanning Stage (PN 432029-9904-000)

• Piezo Stage (PN 432027-9001-000)


Photometrics Prime BSI

Orca-Flash4.0 V3

Useable but not preferred:

Axiocam 506 mono (4.5um per pixel is lower than our recommendation. QE low for Cy5 and too low for optimal AF750 signal)


Plan Apochromat 20x Zeiss

• (PN 420650-9901-000) Older model/Discontinued

• (PN 420650-9902-000) Latest version

Spill Guard

Aqua Stop II f/ AxioObserver

Field Diaphragm

Square FD (PN 1140-737)


Akoya-provided CODEX Acquisition computer

Dark Room

The Zeiss Axio Observer needs to be situated in a dark room

Light sources and Filters

The use of an LED or Halogen light source will determine the use of either Filter cubes or an LED filter. Check with your Zeissrepresentative to confirm the specific Filter cubes or Filter LED.

The information on the dye sets used for CODEX can be found here

Light Source Options

Corresponding Filter Sets

Illuminator HXP 120V

Filter Cube options

• DAPI -Filter set 49 (488049-9901-000)

• FITC - Filter set 38 (000000-1031-346)

• TRITC - Filter set 43 (000000-1114-101)

• Cy5 - Filter set 50 (488050-9901-000)

• AF750 - Only LED Filters recommended from Zeiss

Solid-State Light Source Colibri 7

• PN 423052-9710-000

• Type RGB-UV

• Not for use with AF750

Filter set 90 HE LED

• PN 489090-9110-000

• Not for use with AF750

Solid-State Light Source Colibri 7

• PN 423052-9770-000

• Type FR-R[G/Y]BV-UV

• Use with AF750

Filter set 112 HE LED

• PN 489112-9110-000

• Use with AF750

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