Collection of plugins for OrganoidTracker to measure fluorescence. Integrates with existing cell tracking data, and allows you to measure intensities in a variety of ways, normalize them, and plot them.
- Using a circle or sphere of a set radius around existing cell positions.
- Using a vertex model: every pixel is assigned to the closest cell position.
- Using an existing segmentation image, obtained by some external program.
- Using existing metadata, obtained by some other plugin or program.
- Using the built-in scaled Cellpose-SAM-based segmentation method.
- Using the built-in intensity threshold-based segmentation method.
You can store multiple intensities, all under their own name.
- Multiply all intensities with a single factor so that the median is 1.
- Do a background correction: the background per pixel is set such that the lowest intensity is 0.
- Do a Z correction or time correction: for every Z-layer or time frame, all intensities must have a median of 1.
- All normalizations are stored separately from the raw intensities, and can be undone at any moment.
- Plot the intensities over time to check for bleaching.
- Plot the intensities by Z-layer to check for scattering.
- Plot the intensities by cell cycle to check for cell cycle effects.
- Plot the intensities in color on top of the image, to check for all kinds of aberrations.
- Plot a lineage tree colored by intensity.
- Plot the intensities for a single selected cell (or multiple) over time.
- CSV/TSV file with time points in rows, cells in columns.
- CSV/TSV file with cells at a single time point in rows, and intensities in columns.
First, make sure you have installed OrganoidTracker, and have a dataset & images loaded where you want to measure intensities. Then, open OrganoidTracker, and use File -> Install new plugin. Click on one of the folders that appears in the submenu, or add a new folder for plugins. Then, place all plugin_-files from this repository (download them here) in that folder. Then, back in OrganoidTracker, use File -> Reload all plugins.
Now a new menu will appear: the Intensity menu. From this menu, you can first record the intensities, then normalize them, and then plot them.
Please see the CellPhenTracker documentation. The documentation provides detailed information on how to use the software, including segmentation, recording intensities, background corrections, normalizing intensities, and ratiometric intensities..