Filopodia Counter is a script for automated filopodia counting from single cell images. It expects a multichannel image (2-4 channels). The cell needs to be stained with at least two markers, one that indicates filopodia tips and another that defines the cell area.
Figure 1: Example image for filopodia counter. In the image the cell body had been detected using an actin dye (white) and the every filopodia tip has been detected by staining myosin 10 (magenta).
Filopodia counter in dependent on Fiji-plugins MorpholibJ and BioFormats. Please subscribe to these through the Fiji updater.
- Download the macro filopodia-counter-v4.ijm from this repository and drag-and-drop it into Fiji. Click Run. User interface opens.
Figure 2: User interface of the Filopodia counter
- Add files to be corrected. You can count filopodia in just one image or add multiple images. All these images will be processed with the same parameters.
- Select the channel with the filopodia stain (options C1, C2, C3, C4).
- Select the channel with the cell body stain (options C1, C2, C3, C4).
- Select the path to results folder.
- Select prominence (= signal relative to the local background). Higher prominence detects less filopodia tips.
- Click OK
The script will output
- CSV file containing the name of each processed file
- Quality control image of each processed image
Figure 3: Filopodia counter saves a QC image of each quantified cell. This image has each counted filopodia circled in yellow. Prominence used in this image was set to 2000. Example image available in this repository.
Current version: Filopodia-counter-v4
This plugin is part of the Bioimage Analysis Toolbox created by Turku BioImaging, a broad-based, interdisciplinary science and infrastructure umbrella that aims to unite bioimaging expertise in Turku and elsewhere in Finland. Turku BioImaging is jointly operated by the University of Turku and Åbo Akademi University.
For plugin support, file an issue in this repository.
For more information, email image-data@bioimaging.fi
