GUI Tour ======== This page walks through every panel of the exo2micro GUI, top to bottom. It's the reference you come back to when you're not sure what a particular control does. .. todo:: Add an annotated screenshot of the full GUI here, with callouts labelling each panel. Place it at ``docs/source/users/_images/gui_overview.png``. .. Overview image placeholder .. .. image:: _images/gui_overview.png .. :alt: exo2micro GUI overview .. :width: 100% Input Selection --------------- This is where you pick which samples and dyes to process. **Samples** and **Dyes** are simple text areas — one entry per line. Processing runs every sample × dye combination. **Auto-detect** scans your raw directory for sample subfolders and extracts likely dye names from the filenames. Saves typing when you have many samples. **Survey raw channels** reads a small central crop from every raw TIFF and reports which RGB channels carry signal. This is a pre-flight sanity check — run it once at the start of a new dataset to confirm exo2micro's automatic channel detection will pick the right channel for each dye. Scale ----- The **Scale** dropdown controls how exo2micro estimates the scale factor used to subtract the pre-stain background: - **Auto (Moffat fit)** — the default. A Moffat profile is fit to the log-ratio distribution and the peak is used as the scale. Works well for most samples. - **Auto + ratio percentile** — the Moffat fit still runs, and *in addition* a second difference image is computed using a chosen percentile of the log-ratio distribution as the scale. A text box appears for you to enter the percentile (accepts decimals, e.g. ``99.1``). - **Auto + manual override** — the Moffat fit still runs, and *in addition* a second difference image is computed using an exact scale value you type in. - **Auto + percentile + manual** — produces all three. See :doc:`scale_methods` for guidance on when to reach for each. Execution Options ----------------- **Parallel (multiprocessing)** — check this to run multiple samples concurrently. For small batches (1-3 samples) the overhead of starting workers often makes serial faster; for larger batches parallel is usually a big win. **Workers** — how many parallel worker processes to run. Rule of thumb: ``workers × peak RAM per sample < your total RAM``. Start with 4 and adjust based on what your machine can handle. **Force rerun (ignore checkpoints)** — normally exo2micro skips any stage whose checkpoint already exists on disk. Checking this box re-runs everything from scratch. **From stage** — where to start. ``Auto (resume)`` picks up from the latest checkpoint. Pick a specific stage when you've changed a parameter that only affects that stage onward. For example, if you want to try a different ``scale_percentile`` value, pick stage 4. **To stage** — where to stop. Useful if you only want to regenerate the diagnostic plots (stop at 4) without touching alignment. **Show diagnostic plots inline** — displays the stage-4 diagnostic plots in the notebook as each sample finishes, with short captions explaining each. Turn it off if you're batch-processing dozens of samples and don't want the output cell to balloon. Advanced Parameters ------------------- Collapsed by default. When expanded, shows every tunable parameter organized into four tabs (one per pipeline stage). Each widget shows the parameter's short abbreviation (used in filenames) and a one-line description. Most users never need to touch these. If you do, see :doc:`../developers/parameters` for a full reference. The three action buttons ------------------------ **▶ Run Pipeline** — kicks off processing on the current sample/dye selection. **📋 Check Status** — prints a checklist showing which checkpoint files exist on disk for each sample × dye combination (under the current parameter settings). Useful for seeing where you left off. **↺ Reset Params** — clears any advanced parameter changes and restores defaults. Parameter Comparison -------------------- A convenience for sweeping one parameter across several values. Pick a parameter from the dropdown, enter comma-separated values (e.g. ``10, 15, 20``), and click **Compare**. exo2micro re-runs the affected stage for each value on the first sample × dye combination and shows the results side by side. If **Save variants to disk** is checked, each run's checkpoints are written with the non-default value embedded in the filename (e.g. ``02_icp_aligned_pre_bw10.tiff``), so variants coexist without overwriting each other. 🔍 Zoom & Inspect ----------------- See :doc:`zoom_and_inspect`. 👁️ Blink Comparison ------------------- A visual tool for checking alignment quality. Load two alignment checkpoints — typically the stage-1 post-stain and either the stage-2 ICP-aligned pre-stain or the stage-3 interior-aligned pre-stain — then click the **Blink: A ⇄ B** toggle to flip between them at any region of interest. Good alignment means structures barely shift when you flip. Bad alignment means things jump around. Workflow: 1. Enter your sample and dye. 2. Pick image A (usually **Post, reference, stage 1**) and image B (usually **Interior-aligned pre, stage 3**). 3. Click **Load**. Both images are loaded as downsampled previews. 4. Use the Row / Col / Size sliders to frame a region of interest (a conspicuous feature in the sample is ideal). 5. Click the **Blink: A ⇄ B** toggle button repeatedly to flip between the two images. Features that stay in place are well-aligned; features that shift indicate residual error. To diagnose where in the pipeline an alignment problem came from, compare stage 2 (ICP) against stage 3 (interior). If stage 2 is already bad, the boundary alignment failed and you want to look at ``boundary_width`` / ``boundary_smooth``. If stage 2 is good but stage 3 is bad, SIFT matching in the interior went wrong; check ``interior_blur_base`` or ``interior_min_inlier_ratio``. Progress bar and output ----------------------- As the pipeline runs, the progress bar tracks total tasks completed. The output area below shows real-time text from each pipeline stage plus the inline diagnostic plots (when enabled) and the final summary table. The summary table shows the Moffat scale for every completed run, plus — when you used ``scale_percentile`` or ``manual_scale`` — extra columns for those alternative scales.