Zeiss AxioZoom Macroscope

Metadata Instrument Identifier: ninc-zeiss-axiozoom

If you are annotating your data in preparation for data deposit or format conversion (to Neurodata without borders or other file type for long term preservation) please include the above identifier to indicate the data was taken with this instrument.

Paper Acknowledgement Section Suggested text:

If you are publishing your work and have used NINC resources in your project please use the following text including the persistent identifier for NINC (Research Resource ID, RRID):

This work was supported by resources made available through the Dynamic Brain Circuits cluster and the NeuroImaging and NeuroComputation Centre at the UBC Djavad Mowafaghian Centre for Brain Health (RRID SCR_019086).”

Paper Methods Section Example Microscope Description:

To describe the NINC Zeiss AxioZoom Macroscope in your paper’s methods section please modify this example: “Images were collected on a Zeiss AxioZoom Macroscope equipped with a Hamamatsu Orca Flash 4 camera. Fluorophores were excited standard fluorescent filter cubes for <filter cube options, DAPI, FITC, Texas Red and/or Cy5> with with a <1.0 or 2.3X> objective lens.”

The physical scale of images from the NINC Zeiss AxioZoom Macroscope should be obtained from the .czi file metadata as they depend on the state of the zoom optics acting in combination with the Please contact Jeffrey LeDue (jledue@mail.ubc.ca) if you need help finding this information and tailoring the above statement.

Suggested Software:

The NINC Zeiss AxioZoom Macroscope saves images in Zeiss’ .czi format. Exporting tiffs and jpegs from the Zeiss ZEN acquisition software is not recommended as this can cause loss of metadata (e.g. the physical scale of the image). Please download and install the Fiji versions of imagej. Fiji uses the Bio-Formats importer to work directly with .czi files.

Access and Training:

Access to the NINC Zeiss AxioZoom Macroscope is restricted to trained users from NINC member labs. If your lab needs NINC membership please contact Daphne Druick in DMCBH Administration (ddruick@mail.ubc.ca) and cc Jeffrey LeDue (jledue@mail.ubc.ca) to arrange payment of membership fees. Training sessions are included in the NINC membership fee. Please contact Jeffrey LeDue (jledue@mail.ubc.ca) to arrange a training session.