Imperial College Research Software Community Newsletter - June 2021

Hello RSEs! Like in a weird time machine, we are finally experiencing suspended events from the past: Euro 2020 now and soon Olympics 2020. For tennis lovers, Wimbledon is finally happening. So, a great time for sports. And a great time for practising them as well. It is a pity that we are not also able to enjoy the weather from summer 2020 that I’m sure all of us remember as much better than the current one. But probably it is just a false biased memory… ;)

In any case, let’s enjoy this summer as much as possible, staying active, meeting friends and relatives, and having some good times. And when meteorology fails us, we can find shelter in our RSE newsletter, with many events, blog posts and videos to keep us busy and entertained.

Stay safe!

In this month’s newsletter:

Dates for your diary

RSE Bytes


Blog posts, tools & more

Research Software of the Month

This month the spotlight is on DeepMedic, an efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans developed within the BioMedIA group and listed in Imperial’s Research Software Directory. The research was initially presented in the article “Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation” and ranked first at the Ischemic Stroke Lesion Segmentation (ISLES) challenge for the sub-acute ischemic stroke lesion segmentation (SISS) category, MICCAI 2015.

DeepMedic can process NIfTI images, a very common neuroimaging file format, to detect and segment structures. It uses 3D Convolutional Neural Networks that can be created and trained with custom data by providing properly labelled examples. It is available Open Source and the GitHub repository contains clear instructions on how to setup DeepMedic (including NVIDIA CUDA) and datasets that can be used to check the correct behaviour of the system.

A specific section provides information about the steps required to run DeepMedic with other data.

Some reminders…

RS Community coffee continues weekly via Teams - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.

See the Research Computing Service’s Research Computing Tips series for a variety of helpful tips for using RCS resources and related tools and services.

Get in Touch, Get Involved!

Drop us a line with anything you’d like included in the newsletter, ideas about how it could be improved… or even offer to guest-edit a future edition!

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This issue of the Research Software Community Newsletter was edited by Stefano Galvan. All previous newsletters are available in our online archive.