Quickstart

This page gets you from zero to a first difference image. It assumes you’ve finished Installation and have at least one sample’s raw TIFFs in place.

Launching the GUI

The easiest way to use exo2micro is the interactive notebook GUI. Start a Jupyter notebook (jupyter lab or jupyter notebook), open exo2micro_notebook.ipynb, and run the two setup cells. You should see the exo2micro interface appear.

You can also launch the GUI from any notebook cell:

from exo2micro.gui import launch
gui = launch(
    output_dir='processed',   # where results are saved
    raw_dir='raw',        # where your raw images live
)

Survey your raw channels (recommended)

Before processing, click Survey raw channels in the GUI. This reads a small central crop from each of your raw TIFFs and reports which RGB channel(s) actually carry fluorescence signal.

This matters because exo2micro’s image loader auto-detects which channel has the dye signal. Running the survey once up front catches problems like “I thought SybrGold was in the green channel but actually it’s in red” before you waste time on a full run.

Picking your samples and dyes

Enter one sample name per line in the Samples box (e.g. CD070) and one dye name per line in the Dyes box (e.g. SybrGld_microbe). Or just click Auto-detect — it scans your raw directory and fills both boxes in.

Every sample × dye combination will be processed.

Picking a scale method

The Scale dropdown controls how exo2micro estimates the pre-stain scale factor. For your first run, leave it on Auto (Moffat fit). Come back to Scale Methods later if you need the percentile or manual options.

Running

Click ▶ Run Pipeline. For each sample × dye:

Stage 1 — Padding. Raw images are loaded and placed on a common canvas.
Stage 2 — Boundary alignment. exo2micro finds the best rigid alignment using the sample outline.
Stage 3 — Interior alignment. The alignment is refined using SIFT features inside the sample.
Stage 4 — Diagnostics. The background scale factor is estimated and the difference image is computed and saved.

Each stage saves checkpoints to disk, so if you stop and re-run, exo2micro picks up where it left off.

Watching the diagnostic plots

With Show diagnostic plots inline checked, the GUI displays the five stage-4 plots for each sample as it finishes, along with short captions explaining what to look for. If anything looks wrong, see Troubleshooting.

Finding your results

Everything ends up under processed/:

processed/
  CD070/
    SybrGld_microbe/
      tiff/               ← intermediate and final images (float32)
      fits/               ← same images with FITS metadata headers
      pipeline_output/    ← all diagnostic plots as PNGs

The main result is the difference image:

processed/CD070/SybrGld_microbe/tiff/04_difference_difference.tiff

Positive values in this image = fluorescence that appeared after staining (candidate microbes). Near-zero values = consistent autofluorescent background.

The FITS version has the scale factor and full parameter record in its header for reproducibility:

processed/CD070/SybrGld_microbe/fits/04_difference_difference.fits

Next: GUI Tour walks through every GUI panel in detail, and Interpreting Results explains how to read the diagnostic plots.