Facility Publication Policy

In common with many other microscopy facilities, the AMF follows the Royal Microscopical Society publication guidelines. This means that:

1. Publications must acknowledge the AMF (and named staff if appropriate) when a study uses equipment managed by the Facility.
2. In cases where an AMF staff member has contributed significantly and/or provided non-routine services, they are to be added as co-authors.

We strongly encourage authors to send us manuscripts before publication so we can proofread the relevant methods and descriptions. Imaging methods are often very poorly reported (eLife) in publications. Work coming from the SWC should continue to buck this trend.

Standard acknowledgement

Examples of standard acknowledgement text:

• 'The authors would like to thank the SWC Advanced Microscopy Facility for their assistance with confocal imaging.'
• 'The authors thank John Smith and the SWC Advanced Microscopy Facility for assistance with light microscopy and protocol development.'

Co-authorship

Facility scientists should be listed as co-authors if they contributed intellectually, or contributed non-routine services or techniques. Routine work includes things like user training, microscope maintenance, standard histology, and simple raw data acquisition. Examples of non-routine work include:

• Extensive data analysis; in particular generating figures that appear in your publication or building analysis tools to generate those figures.
• Significant development or optimisation of protocols used in your study. e.g. Validating a new antibody does not count but spending extended time developing and documenting a bespoke clearing, labelling, and imaging pipeline for a novel application does count.
• Building and validating a significant modification to your in vivo imaging pipeline. e.g. Adding a new filter to your rig does not count but helping you construct and validate temporal focusing does count.
• Building significant new equipment. e.g. 3D printing a new sample holder does not count but helping you build a rig for optically tracking mouse toe movements does count.

Facility URL

If you wish to add a web link, you may use swcmicroscopy.com for the Facility itself; this will remain unchanged for the foreseeable future. If you need to link to a specific sub-page, contact us first to confirm it is not likely to be changed or removed in the near future. Avoid linking to our GitHub wiki, as that content is more labile. You may safely link directly to a relevant AMF GitHub repo.

Citing BrainSaw

The serial section equipment in the facility are not associated with a methods paper. You can cite using DOIs and link for the software repositories:

• BakingTray acquisition software: GitHub link, DOI
• StitchIt image assembly: GitHub link, DOI

A reasonable way to cite the equipment in your methods section would be:

Then acknowledge as appropriate.

Your methods section should provide full information on how the images were acquired. An suggestions are provided on the serial section sign-up page.