Imperial College Research Software Community Newsletter - March 2021

Hello everyone & welcome to the March newsletter. Get ready to be amazed by the crazy notion that there’s anything going on outside your four walls!

Dates for your diary

RSE Bytes

Workshop report: Imperial/Sheffield ReproHack - Tuesday 9th March 2021



Blog posts, tools & more

Imperial has positions open for an [RSE Team Lead and Senior RSE (in ICT) and an RSE (R Developer)] (in the School of Public Health). Closing date for the first two jobs is 09/04/21, while the RSE (R Developer) closes on 14/04/21.

Research Software of the Month

This month’s pick is OpenSlide. A recent piece of work I had to do involved processing some slide images to make them available in manageable chunks to a neural network. Virtual slides are large, high resolution (often multi-resolution) images used in digital pathology, and reading them using standard image tools or libraries is a challenge because of their size, and because there’s no universal data format so each vendor implements its own, typically undocumented, formats, libraries, and viewers.

My particular vendor (Hamamatsu) produces files in a format called NDPI, and after struggling for a bit to tile them up with a bespoke command line utility I discovered OpenSlide and its Python binding (its core is C; there’s a Java binding too). The API is very simple; there’s broadly speaking one method that reads a region of the image at the desired position and resolution and makes it available as a PIL image (in the Python case) for further processing.

Some reminders…

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

The Slack workspace also features an #OpenFOAM channel where regular code review sessions are announced (amongst other CFD-related discussions…)

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 Jazz Mack Smith. All previous newsletters are available in our online archive.