Outputs

theatRICS writes analysis results to disk so that intermediate and final outputs can be reused outside the GUI and across sessions.

Output types depend on the workflow, but commonly include:

  • TIFF for image-based correlation outputs

  • CSV for fit curves and summary tables

  • NPZ for stored model arrays and auxiliary numerical outputs

  • SVG for publication-quality figures

  • Excel (.xlsx) for FRAP raw data and summaries

  • TXT / JSON for logs and saved GUI sessions

General output behavior

Per-file outputs

Most analysis tabs write outputs next to the input file or into a nearby Results/ folder.

Batch outputs

For batch workflows:

  • some per-file outputs remain next to each file

  • summary tables may be written once in the outer selected folder

Plot exports

Displayed figures can be exported directly from the GUI, typically in:

  • SVG

  • PNG (depending on workflow and settings)

Image Simulation outputs

The Image Simulation tab writes simulated image stacks as TIFF files.

Typical output

  • simulation_output.tif

Contents

The TIFF contains the generated frame stack.

Display-only outputs

The GUI also shows:

  • first frame

  • last frame

  • average image

  • intensity trace

These are visual diagnostics and are not necessarily written automatically unless exported through the GUI.

RICS Export outputs

The RICS Export tab generates correlation outputs from microscopy image stacks.

Typical outputs

  • RICS correlation map TIFF

  • uncertainty map TIFF

  • optionally corrected image stack TIFF

  • optionally intermediate TIFF files

Common naming conventions

Depending on your worker implementation, file names may include patterns such as:

  • *_RICScorr.tif

  • *_RICSunc.tif

Contents

  • RICScorr — correlation map

  • RICSunc — uncertainty / standard deviation map

RICS Fitting outputs

The RICS Fitting tab produces fitted model results from exported RICS maps.

Typical outputs

  • fit summary CSV

  • NPZ file containing arrays used in fitting

  • SVG figure of the fit

  • optional diffusion map outputs

Common contents of the summary CSV

  • diffusion coefficient

  • model type

  • offset

  • file path

  • optional 1D fit results

Figure outputs

The GUI fit display can be saved as:

  • *.svg

For example:

  • my_rics_map_fit.svg

NPZ outputs

These can include arrays such as:

  • RICS map

  • fitted model

  • residuals

  • optional 1D model and residual arrays

Diffusion map outputs

Diffusion map generation writes spatially resolved fitting outputs.

Typical outputs

  • diffusion map

  • number map

  • brightness map

  • auxiliary arrays stored in NPZ or similar formats

Displayed outputs

The GUI may show:

  • diffusion map

  • brightness map

  • number map

  • representative 1D fits

SFCS outputs

The SFCS tab computes scanning FCS correlations.

Typical outputs

  • correlation curves

  • uncertainty estimates

  • exported plot files

Common plot outputs

For example:

  • *_correlation.svg

Contents

Plots typically contain:

  • G(τ) curve

  • optional uncertainty band

  • intensity traces

  • aligned/original previews

FCS Fitting outputs

The FCS Fitting tab writes outputs for each fitted correlation CSV.

Per-file outputs

For an input base name mycurve and model g2diffSFCS, the software typically writes:

  • Results/mycurve_g2diffSFCS.svg

  • Results/mycurve_g2diffSFCS.csv

  • Results/mycurve_g2diffSFCS_iMSD.csv (if applicable)

Description

Results/<file>_<model>.svg

A publication-quality vector export of the displayed FCS fit figure.

Results/<file>_<model>.csv

A table containing:

  • tau

  • G

  • sigma G

  • fitted correlation curve (cc Fit)

Results/<file>_<model>_iMSD.csv

Written only for models where iMSD is meaningful.

Contains:

  • tau

  • iMSD

Batch summary output

In recursive batch mode, the software writes one summary CSV in the outer selected folder, typically:

  • Results/<model>_fit_summary.csv

This summary contains one row per fitted file.

Typical summary columns

Depending on model:

  • diffusion coefficient(s)

  • particle number / amplitude parameters

  • blinking parameters

  • offset

  • characteristic times

  • BIC

  • goodness-of-fit statistics

  • original filename

FRAP outputs

The FRAP tab writes outputs next to each analyzed CZI file.

For an input file such as:

sample1_FRAP.czi

the software typically writes:

  • sample1_FRAP_raw_data.xlsx

  • sample1_FRAP_summary.xlsx

  • sample1_FRAP_overview.svg

*_FRAP_raw_data.xlsx

Contains:

  • frame index

  • time

  • raw ROI intensities

  • control-normalised traces

  • model fit values for FRAP ROIs

*_FRAP_summary.xlsx

Contains:

  • ROI metadata

  • fitted parameters

  • mobile fraction

  • immobile fraction

  • diffusion coefficient in px²/frame

  • diffusion coefficient in µm²/s (if pixel size is available)

  • recovery time constant

  • half-time

  • optional imaging bleach decay constant

  • warnings

*_FRAP_overview.svg

A vector export of the FRAP display figure shown in the GUI.

Optional batch-level outputs

If a condition-summary workflow is used, additional condition-level outputs may be produced, such as:

  • FRAP_condition_summary.png

depending on how batch aggregation is configured.

Logs and session files

The Results & Logs tab allows saving auxiliary outputs.

Log export

  • *.txt

Contains the textual log shown in the GUI.

Session export

  • *.json

Contains saved GUI parameters and session state.

Plot export

The GUI can export currently available figures, typically as:

  • PNG

  • SVG

depending on workflow and implementation.

Vesicle Finder outputs

Crop outputs

For a CZI file named sample.czi, square crop outputs are written to:

sample_vesicle_crops/
    vesicle_1.tif
    vesicle_3.tif

Each TIFF contains all selected frames stacked along axis 0 with shape (n_frames, crop_size, crop_size).

Straightening outputs

For a CZI file named sample.czi, straightening outputs are written to:

sample_straightened/
    vesicle_1_straightened.tif
    vesicle_1_intensity_profile.csv
    vesicle_1_total_intensity.csv
    straighten_overview.svg

File

Contents

*_straightened.tif

3D TIFF: (n_frames, thickness_px, n_angle_points) — the unrolled membrane

*_intensity_profile.csv

Mean intensity across thickness for each angle and frame

*_total_intensity.csv

Total membrane intensity per frame

straighten_overview.svg

Combined display figure

Debug outputs

When debug saving is enabled, intermediate images are saved to:

sample_debug/
    01_raw_normalized.tif
    04_binary_after_threshold.tif
    05_binary_dilated.tif
    06_interior.tif
    07_distance_interior.tif
    08_distance_smooth.tif

Notes on file placement

Local Results/ folders

Several workflows write outputs into a Results/ folder next to the input file.

Outer-folder summaries

Recursive batch processing may place summary outputs in the outer selected folder instead of repeating them in every subfolder.

This is especially useful for:

  • FCS fitting batch mode

  • condition-level FRAP aggregation

Reproducibility

Because theatRICS writes numerical outputs in standard formats such as CSV, TIFF, NPZ, and Excel, the results can be:

  • reloaded into Python or MATLAB

  • inspected manually

  • included in downstream analysis pipelines

  • used to regenerate publication figures