Codes

• 'Blank_frame.m' is for blank frame detection and video reconstruction.
• 'Intensity_variation.m' is for detecting and reconstructing distorted frames and producing a new video.

Fiji Plugins

This algorithm is deployed as a Fiji plugin. To run the plugin:

• Install Fiji here
• Download .ijm macro script in the folder "Plugins_Fiji"
• Add the script to the plugins menu in Fiji application:
  The macro must be saved in Fiji.app/scripts/ (or a subdirectory thereof) [^1]
  The file extension of the macro file must be .ijm
  The filename must contain an ‘_’ (underscore) character.
  

Note that, as opposed to plain IJ1 [^2], this approach allows you to register your macros and scripts in any menu. So, if for example, you place your macro script in Fiji.app/scripts/Edit/My Own Submenu, it will appear in Edit>My Own Submenu>

[^1] In Fiji, it is also possible to place scripts in another legacy location: Fiji.app/plugins/Scripts/
[^2] In plain IJ1, the macro can have either an .ijm or .txt, and must be placed in the /plugins/ directory.

Exaplanation of adding a script to the plungin menu can be found here

Acknowledgement

• This work is supported by the Scientific and Technological Research Council of Turkey (TUBITAK) under grant no 119E578.
• The data used in this study is collected under the Marie Curie IRG grant (no: FP7 PIRG08-GA-2010-27697).
• The dataset contain cell motility, macrophage behaviours, and some other experimental Phase Contrast Microscopic (PCM) images.

Citation

• If you find the work useful, please consider citing the paper:

@inproceedings{ucar2022detection,
title={Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images},
author={Ucar, Mahmut and Iheme, Leonardo O and Onal, Sevgi and Ozuysal, Ozden Y and Okvur, Devrim P and Toreyin, Behcet U and Unay, Devrim},
booktitle={2022 Medical Technologies Congress (TIPTEKNO)},
pages={1--4},
year={2022},
organization={IEEE}
}