A collection of ImageJ macros for analysing macrophage response to bacterial infections in zebrafish
Automatically detects areas of bacterial infection and allows user to select which regions are considered sites. Assumes the infection site is the same for all time.
- Open a single channel image stack in Fiji (or split channels from a multichannel image stack)
- Run macro
- When prompted either select single ROIs and add them to the manager or select groups of ROIs and use More...> OR (Combine) to group them and then add the new group to the manager. Click OK.
- Convex hulls of the selected regions will be output to the ROI manager
Huang threshold is used, this may be to be changed depending on data
Identifies tracks (from TrackMate analysis) which intersect ROIs in the ROI manager.
- Open ROI manager and add ROIs (or use ROIs from InfectionSites.ijm)
- Open .csv of the Spots TrackMate results in Fiji
- Run macro
- Number of windows equal to ROIs will be opened. Each window will contain a list of the track IDs that contain a spot which intersects the ROI at any time.
Pulls relevent information about the tracks of interest
- Open list of track IDs for tracks of interest in Fiji (or use opened windows from TrackIntersectRois.ijm)
- Open .csv of Tracks TrackMate results in Fiji
- Run macro
- Will open window containing a subset of information about the requested tracks, track ID, track displacement and track mean speed
Other values from the Tracks.csv file can be added.
Automatically measure the area and intensity. If image has multiple channels it will analyse all the channels.
- Run macro
- Use dialog box to select input folder, output folder and file suffix
- Saves results and rois to output folder
Uses same automatic threshold for everything, may need to be different for each image/channel