Imaging Mass Cytometry Database
Imaging Mass Cytometry Database
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The purpose of the database
Track which tissues and species users are working on. This will allow users working in similar areas to collaborate.
Track which lab groups own which antibodies. This will allow potential users to approach labs with antibodies they would like to trial in their tissue.
Record conditions in which antibodies work. This will involve a full record of which tissues, species, fixation methods etc were used in each Hyperion run, and which antibodies stained successfully. This sharing of optimisation runs between users will allow us to all spend less time optimising.
Record conditions in which antibodies didn’t work. Runs in which staining didn’t work will also, ideally, be recorded.
Allow users to enter new antibodies and Hyperion runs to the database. This will keep the database up-to-date and allow the resource to grow.
Keep a track of what users are working on. This is to identify areas of potential collaboration.
Why do we need a database?
Imaging mass cytometry is a new and powerful technology, but it is not without its limitations:
Buying an entire antibody panel is expensive. Especially if you’re not sure the antibodies will even work on your tissue, and there aren’t yet a huge number of published papers with validated panels.
Optimising a panel may be a lengthy process. Getting 35+ antibodies to stain optimally is no mean feat, and will likely require a significant amount of resources and time to get right for each user.
The machine has low-throughput. The Hyperion images the slides at quite a slow speed, and the Hyperion time is currently shared with the Helios CyTOF.
Therefore, without considerable co-operation between users, it’s likely that there will be a significant amount of overlap in the optimisation processes undertaken by different users, and so wasted time and resources. Ideally, we want to spend the minimum amount of time/resources on optimisation!
Currently, database can be freely viewed by anyone with this link. Data can be freely sorted, grouped or filtered to find specific information.
Editing rights can be granted on request.
Users research interests, training records and contact details.
If you are a new or existing user, please add your details here to be included in the usergroup.
If your lab group does not appear, add them here.
Comprehensive information about antibodies, including clones, metal conjugations, owners and optimisation information.
Antibodies can be added in bulk (e.g. from an Excel sheet) by emailing support.
Details and results from optimisation runs, including tissue type, species, staining protocols, and example data.
The antibodies in your panel must first be added to the database.
Navigating the database
The database is built on Airtable, which allows the data to be visualised in a spreadsheet. Navigate and treat this like any other spreadsheet.
The data is spread over 4 tabs: Antibodies, Runs, Users and Lab Groups.
In each tab, you can select premade Views on the left hand panel. These apply premade filters and groups to the data, for example allowing you view only mouse antibodies.
You can also filter, group or sort the data by clicking on any of the relevant buttons.
When followed from this website, the information is all read only, so none of the underlying data will be affected.
Contributing to the database
New users should add themselves and their lab groups.
Antibodies should then be added to the database using the form.
Runs in which the antibodies are used can then be added.
Alternatively, data can be added manually and edited by those with specific access to the database. For example, if you already have an Excel spreadsheet with all your antibodies, just email that and we can quickly copy and paste them in.
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