Coding resources
This web page is a hub for resources related to coding and data analysis for the Life Sciences environment. We (SLIM) provide specific support for image analysis, the information below is intended as a directory of resources, and those involved are doing this on a voluntry basis.
Slack 'Code Club'
SoLS Code Club. Slack is a cloud-based chat and messaging application that can also be used to share code, links and other resources. Our use of Slack aims to create a network of University of Nottingham life-science coders sharing tips, advice and code. The motivation is to make data-analysis more efficient (reusing code and knowledge), open up new types of analysis (to those less experienced) to increase the richness of data and so the impact of peoples work. Anyone with an @nottingham.ac.uk email address can join. Currently we have channels for Fiji, R, Python, GitHub, MatLab, Java and Image Analysis as well as areas for general discussion. Using Slack, rather than email, moves the cumulative knowledge to a searchable log and reduces the impact to those times when people want to engage.
Seminars and workshops
We run occasional activities for developing knowledge in coding and related areas, details below.
Twitter
A number of people associated with coding in the School are on social media, you might like to follow @ChrisGell_Notts_SLIM for some general coding and inage-analysis related tweets.
Language/Software Specific Resources
Fiji (ImageJ2 Macro)
- Fiji (Fiji is just ImageJ) www.fiji.sc Fiji is an open-source image processing package—a "batteries-included" distribution of ImageJ (https://imagej.net/), bundling a lot of plugins which facilitate scientific image analysis.
- Fiji has a thriving community of plugin developers and is highly extensible through scripting.
- SLIM maintain a Fiji update-site that we use to distribute code.
- SLIM run worshops for training in Fiji.
- The SoLS Code Club has a Fiji channel.
- UoN Fiji gurus are: Chris Gell
- Slides from the code-club launch now avaliable on the SLIM GitHub site.
Cell Profiler
- The Cell Profiler website.
- CellProfiler is free, open-source software for quantitative analysis of biological images.
- CellProfiler is especially suited to the analysis of High Throughput assays.
- The image.sc forum hasw a section dedicated to Cell Profiler.
- Slides from the code-club launch now avaliable on the SLIM GitHub site.
- R is a free software environment for statistical computing and graphics.
- The website of The R Project..
- Slides from the code-club launch now avaliable on the SLIM GitHub site.
A number of UoN staff and students maintain GitHub repositories, SLIM can host your code on out GitHub.:
ilastik
ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis