Hi everyone 👋

Unfortunately, I haven't had time to look after this repository for a (long) while. However, based on citations and traffic to repositories, I see there is still interest in PHANTAST. If you would like to become a maintainer, please create an issue here on Github, or email me: hello [AT] nicjac [DOT] dev.

I hope you find this code useful. Thanks!

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

With the ultimate goal of being plateform agnostic, PHANTAST is currently available as a standalone GUI, MATLAB code, and FIJI plugin.

IMPORTANT: You are currently browsing the PHANTAST for MATLAB repository, which also hosts a standalone GUI application. If you are interested in the PHANTAST for FIJI/ImageJ plugin (offering similar functionality), please naviguate to the corresponding repository.

PHANTAST was first described in an open-access paper where it was used to non-invasively monitor proliferation, cell death, growth arrest and morphologyical changes in adherent cell cultures based on phase contrast microscopy images.

• Microscope users / researchers: get the most of your phase contrast microscopy images and start generating quantitative data right away using our graphical user interface tool that does not require any image-processing knowledge
• Developers: study, re-use and/or improve on our segmentation algorithm. We are keen on seeing what you can do with it!

• Head to the release page and download the latest release of the PHANTAST for MATLAB and the corresponding standalone GUI applications. Alternatively, you can checkout the code and use it directly from the command line or part of your scripts/functions.
• The wiki contains a tutorial to get you started with PHANTAST for MATLAB
• You can get in touch with us through various means:
  • Use the issue page to report problems with the plugin
  • Head to the getting in touch page for more traditional contact means
• PHANTAST is also available as a plugin for the very popular FIJI/ImageJ biomedical image processing package.
• If you use PHANTAST for your research, please consider citing our papers

Generating quantitative data from PCM images is generally a tedious experience. Manual processing is time-consuming and error-prone while the use of general purpose image processing software package can be frustrating due to their complexity and the need to tweak parameters.

Clearly, PCM image processing is currently much more difficult than it should be. PHANTAST was developed by researchers who are in the laboratory and understand the need for a convenient tool that delivers uncompromising performance.

Key features of PHANTAST:

• PHANTAST enables culture confluency determination and cell density estimation (even for colony-forming cell lines) based on unlabelled PCM images.
• High performance. PHANTAST is based on image processing algorithm specifically developed with PCM images features in mind, more specifically the low contrast between the cells and the background, and halo artefacts surrouding cellular objects.
• It is free. Do not spend a large portion of your research budget on software license.
• It is open. Unlike most commercial products that adopt a black box model, PHANTAST is open and you are encouraged to delve into the code. See something wrong? Think a feature should be implemented? Let us know and join our effort!
• Consistency. PHANTAST has been thoroughly validated using a variety of cell lines, imaging protocols and microscope models.
• Choice. PHANTAST is available as MATLAB code, as a standalone GUI tool and as a FIJI plugin.