- The latest version of the plugin can be downloaded from the Releases page.
- Place this .jar file into the /plugins directory of the your Fiji installation.
- It's necessary to manually install the StackReg_ plugins that are used for image registration. This can be done by enabling the BIG-EPFL update site in the Fiji updater.
- In Fiji, run the plugin from Plugins > Wolfson Bioimaging > RelateCells > RelateCells
- You'll be presented with a parameters dialog:
- "Fluorescence channel name" is the unique part of the filename corresponding to fluorescence channel images. For example, in the name "180216_Red_B1_4.avi" this is simply "Red".
- "Phase contrast channel name" is the unique part of the filename corresponding to phase-contrast channel images. For example, in the name "180216_Phase_B1_4.avi" this is simply "Phase".
- "Measure phase contrast fluorescence" is an option allowing fluorescence intensity coincident with the phase contrast cells to be measured. If enabled, the unique filename is specified as above.
- "Border width (%)" allows for a border region to be ignored. This is necessary to remove accidental detection at the image edge following image registration.
- "DoG filter radius (px)" is the sigma (radius) for the difference of gaussian filter run on the phase contrast channel. It should be set to match the approximate cell radius.
- "Threshold multiplier" allows the fluorescence cell detection threshold to be shifted up or down relative to the automatically-identified threshold value.
- "Minimum cell size (px^2)" and "Maximum cell size (px^2)" allow small or large objects to be ignored from fluorescence cell identification.
- "Max. edge-edge distance (px)" is the maximum spatial linking distance for fluorescence and phase-contrast cells.
- "Max. centroid-centroid distance (px)" is the maximum spatial linking distance for tracking fluorescence cells in time.
- "Detection radius (px)" and "Threshold" correspond to the spot detection parameters in the TrackMate LoG detector.
- The current plugin progress is displayed in the log window. Once the analysis has run, "Complete" will be displayed.
This plugin is still in development and test coverage is currently incomplete. Please keep an eye on results and add an issue if any problems are encountered.
A list of bundled dependencies along with their respective licenses can be found here.