Here’s a non-exhaustive list of useful opensource imaging tools I use frequently or have come across and found intriguing/potentially useful.
- FIJI for image processing and analysis. Java based. Can code macros on most popular coding language, as well as imageJ’s own scripting language. I use this all the time. I swear by it. It’s not as clean and fancy as commercial imaging software, but its solid for free, open-source, and constantly being upgraded.
** Note: I have another post about FIJI plugins that I am a huge fan/user of** - Micromanager is an image acquisition platform built onto imageJ2.
- CellProfiler is a large scale data analysis software available from the Broad institute.
- KNIME is a machine learning based image analysis pipeline development software. Very openended and applicable to a number of useful fields beyond microscope.
- Ilastik is a machine learning based image segmentation platform.
- OpenSPIM is an opensource platform for light sheet microscopy
- SciKitImage is a python library for image analysis.
- ICY is an open source bioimage analysis platform. Like KNIME, workflows can be designed graphically, but also integrates really well with python and java for scripting.
- ImagePy is an open source python library for image processing
- ImgLib2 is a java-based multidimensional image processing library.
- ImJoy offers deep learning based classification and segmentation for image processing.
- ClearControl: Still in development. Will be an open-source light sheet microscopy (SPIM) image acquisition software.
Forum for this stuff is all at https://forum.image.sc/
This list is constantly growing. I will try to keep a repository of things as I find them.
