Frequently Asked Questions

Frequently Asked Questions

1) Do I need any special software or licenses?

2) What algorithms are being used?

3) How do I install the algorithms?

4) Is it possible to add more algorithms? Can I propose one experiment to be analysed?

5) Is it possible to contribute with algorithms?

6) Are there any test data?

7) Are there any disclaimers?



1) Do I need any special software or licenses?

We are releasing all the software as matlab m-files, which are free to use, modify and adapt (subject to cite our publications if you find them useful for your research, please also read the disclaimers below). To be able to use them, you will need a valid license of MATLAB, which can be obtained from Mathworks. Most Academic Institutions will have site licenses of MATLAB. Contact your IT department regarding MATLAB.


2) What algorithms are being used?

The algorithms have been specifically developed for each task and some of them have been published. The publication at PLOS ONE has a general description of the algorithms. We have made an effort for the code to be readable and therefore easy to adapt and change (one function to track, one function to segment, one function to determine threshold levels, etc.).

It is important to remember that every algorithm will assume certain conditions. We have derived these algorithms from our particular data sets and computers, and even when we have made an effort to make then compatible for other sources/operating systems, there may be compatibility problems, for which we are not liable in any way, please read the disclaimers below.
In summary, algorithms do not work under every imaginable situation, but what they do offer is a consistent processing for all the images they are applied to.


3) How do I install the algorithms?

Download the algorithms from the link in the SOFTWARE tab, choose "SAVE". This will save a zipped file with all the m-files. Place them in your computer in a suitable location (NeutrophilPackage or PhagoSight for instance) and when you start MATLAB, select File > Set Path. Click ADD FOLDER and navigate to  NeutrophilPackage (or which ever name you chose) and click OK. Click then SAVE and CLOSE. After this, you can use the files as described in the User Manual.


4) Is it possible to add more algorithms? Can I propose one experiment to be analysed?

Yes. We are constantly working on new algorithms and there are several algorithms on the pipeline at the moment. If you have an interesting experiment that produces images that require quantitative analysis, contact us and we will study the case. We cannot promise that an algorithm would be produced immediately but we will try. Send an email to (please replace {at} and {dot} when sending the email) phagosight {at} phagosight [dot] org ; with a description of your data and the processing required together with one or two example images.



4) Is it possible to contribute with algorithms?

Of course! We would love to hear from anyone that has used the software, with success or with problems so that we can continuously improve our algorithms. If you have modified the software and would like to share it we will add your files to the package and give you all credit.  Send an email to (please replace {at} and {dot} when sending the email) phagosight {at} phagosight {dot} org   if you have any contribution to be made.


6) Are there any test data?

Yes, there is a section with several synthetic data sets, with different shapes and levesl of noise. We plan to upload more synthetic and real test data sets.


7) Are there any disclaimers?

Yes, of course! The m-files, data and information is provided for educational and informational purposes only, and is not intended for professional purposes. These files are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The authors shall not be liable for any errors or responsibility for the accuracy, completeness, or usefulness of any information, or method in the content, or for any actions taken in reliance thereon. If you find any errors or problems with the programs we should try to fix them but no promise is made.