Temporal-Colour Code — All-LUTs Fiji Macros

Fiji/ImageJ macros that batch-run temporal colour coding on a time-lapse z-stack: each frame is tinted according to its position in time (early frames at one end of a lookup table, late frames at the other) and merged into a single projection, so the result shows where and when signal appeared in the sequence — in the style of Fiji's Temporal-Color Code plugin (Kota Miura, EMBL Heidelberg).

Rather than running the plugin once per LUT by hand, these macros embed its core colour-coding logic directly and loop it over every LUT in its dialog (49 in total), saving one PNG per LUT and closing each result as it goes. The calibration/colour-scale bar is disabled for every run.

Scripts

• TemporalColorCode_AllLUTs.ijm — processes the active z-stack as-is.
• TemporalColorCode_AllLUTs_Reversed.ijm — same, but first duplicates the stack and reverses its slice/frame order, so the colour mapping runs from the last frame to the first instead. Output filenames get a _reversed suffix. The original stack is never modified in either script.

Requirements

• Fiji (ImageJ), with a single-channel z-stack or time series already open.

Usage

1. Open your stack in Fiji and make sure its window is active.
2. File > New > Script..., set the language to IJM, paste in the contents of the macro, and click Run (or Plugins > New > Macro).
3. When prompted, choose the folder to save the PNGs into.
4. The macro loops over all 49 LUTs, saving <LUT name>.png (or <LUT name>_reversed.png) for each into that folder, then closes the result window before moving to the next LUT.

Output

One RGB PNG per LUT, same width/height as the source stack, with no colour scale bar. The original stack window stays open throughout and is left untouched.

Notes

• Projection method defaults to MAX intensity over the full frame range (matching the plugin's own defaults); SUM and WeightedSUM are supported by the underlying logic but not exposed as a loop option here.
• Written against an older ImageJ macro interpreter without try/catch support — if a single LUT fails, the whole run stops rather than skipping it.