Scan-o-matic (program) and scanomatic (python module)

This project contains the code for the massive microbial phenotyping platform Scan-o-matic.

Scan-o-matic was published in G3 September 2016.

Please refer to the Wiki for instructions on use, installation and so on.

We have a newsletter that informs about important changes and updates to Scan-o-matic, you can sign up here.

If you are considering setting up Scan-o-matic at your lab, we would be very happy and would love to hear from you.

Gothenburg University is currently buying further development and service from private company Molflow. Expect to hear more about this soon.

Before you decide on this, the Faculty of Science at University of Gothenburg has included Scan-o-matic among its high-throughput phenomics infrastructure and it is our expressed interest that external researchers come to us. If you are interested there's some more information and contact information here: The center for large scale cell based screeening. It is yet to become listed on the page, but don't worry, it is part of the list.

Current focus

The ability to add new Cell Count Calibrations via UI is being developed.

Completing and securing up the code for the first release of 2.x

Reporting issues

If you have a problem please create and issue here on the git repository. If it relates to a specific project please include the relevant log-files for that project. There are also a set of files that probably is relevant: .project.settings, .project.compilation, .project.compilation.instructions, .scan.instructions, .analysis.instructions... Please also include the server and ui-server log files (those will be localized to a hidden folder called .scan-o-matic/logs in your users directory.

Do however please note, that if you are doing something super secret, the files will contain some information on what you are doing and it may be needed that you go through them before uploading them publically. In this case, only redact the sensitive information, but keep general systematic parts of these lines as intact as possible.