FAQ

Getting started

1. Attend the induction and laser safety training. This takes place on the first Tuesday of each month at 09:45. Just turn up at the Facility, no need to book. We start promptly and if you are late you have to wait until the next session.
2. Start an account on the PPMS Microscope Booking System. Use your SWC (not UCL) login details. If you do not have an SWC account, see SWC IT. The user name must be prefixed with ad\ on the login page, e.g. like this: ad\tomo
3. Contact us via Slack: Peter for general microscopy; Jess for histo; Rob for BrainSaw; Isabell for in vivo 2p; Igor for BrainGlobe and analysis. There are specific channels for most things, which you can join to receive notifications.
4. Please discuss your imaging needs with us before starting the relevant experiments. This can avoid wasted time.

Where are we?

The Facility is located in the SWC on Level B2, immediately to the left as you come out of the lifts. You need to be laser safety trained to have access to the Facility. There is a doorbell to the left of the door.

How to contact us?

Contact us via Slack. Our notifications regarding equipment are sent only via Slack: please make sure you join channels associated with equipment you use.

How do I sign up for BrainSaw?

The BrainSaw sign up details are here.

Citing and acknowledging the facility

The Facility should be properly acknowledged in published work to which it contributed and, where appropriate, Facility staff should be listed as co-authors. Please read our full publication policy before submitting a manuscript.

Do you take samples from external users?

The AMF primarily caters for scientists within the SWC. Since we also conduct a lot of internal technique development, we unfortunately do not have the bandwidth to take on significant numbers of external samples. However:

1. We may be able to generate small quantities of pilot data. Charges apply.
2. We can assist with technology transfer: helping external groups to build our tools.
3. We are very open to collaborations with external groups or facilities, especially where knowledge transfer takes place.

Where do I store my data?

We strongly recommend data are stored on one of the Centre's managed servers. Data on these are safe: they are backed up to tape and the hardware is well monitored. We also strongly suggest you adhere to the following guidelines:

• Store data in your group's shared directory rather than in your own personal user folder. Data kept in your user folder are only visible to you.
• Include your initials in the file names of your images, acquisitions (e.g. brainsaw acquisitions), or in the lowest level folder that holds the images. This helps trace who produced what.
• Store images in a sensible directory structure, e.g. ./margrie/projects/MVF_2023_ThreePhotonValidation/BrainSaw
• Data on the server are backed up to tape. Renaming the folder housing the data or moving the data to a new location will spawn a new backup. i.e. If you have a folder with 200 TB of data and you move it or rename it, you will spawn a duplicate 200 TB backup. Try to settle on a suitable folder structure in advance to minimise the creation of redundant backups.
• For the above reason, avoid routinely placing data in "temporary" locations on the server before moving them on to a final location.

How do I analyse my data?

If you are unsure how to analyse your data, come and talk to us as early as possible. Ideally before you even start data collection. We can help define your question and, if you come before data acquisition, we can often save you a lot of time. There are also these useful resources:

• From microscope to figure by Stephen Royle
• Seeing is believing? A beginners' guide to practical pitfalls in image acquisition, by Alison North
• Tutorial: guidance for quantitative confocal microscopy, by James Jonkman, Claire Brown, Graham Wright, Kurt Anderson & Alison North
• The good, the bad and the ugly, by Helen Pearson

What tools are available for analysing whole-brain imaging data?

If you have whole-brain (3D BrainSaw or lightsheet data), in the first instance we suggest you try the BrainGlobe tools, developed at the SWC with the help of international collaborators. These tools are Python-based and leverage napari. If you have serial mounted slices rather than a true 3D (BrainSaw or lightsheet) dataset, you can look into tools such as ABBA, DeepSlice, SHARCQ, and QuPath.

What data visualisation tools can I use?

There are a variety of data visualisation tools you can use. Common ones:

• Fiji - You can use virtual stacks or the BigDataViewer to navigate large datasets
• Free Imaris Viewer - Imaris now have a stripped down version that is free
• Icy - Fiji alternative
• ClearVolume - Fiji plugin for making pretty transparent volumes.

Perhaps less common alternatives:

• spimagine - Volume renderer
• Fluorender - 3D volume renderer aimed at neuroscientists. Probably can't handle large datasets.
• Knossos - Big data image annotator
• Orbit - Image analysis tool