GUI User Guide

GUI User Guide#

Interactive data preview and processing tools for calcium imaging data.

Quick Start#

uv pip install mbo_utilities
mbo                    # opens file dialog
mbo /path/to/data      # opens specific file
mbo /path --metadata   # metadata only

Features#

  • time and z-plane sliders

  • window functions (mean, max, std, mean-subtracted)

  • scan-phase correction preview

  • multi-ROI statistics

  • contrast controls (vmin/vmax)

  • suite2p processing integration

  • export to .tiff, .zarr, .bin, .h5

Supported Formats#

Format

Description

.tiff

raw scanimage, bigtiff, ome-tiff

.zarr

zarr v3 arrays

.bin

suite2p binary format

.h5

hdf5 files

Note

The full Data Preview widget is only available for raw ScanImage tiffs.

Data Selection Dialog#

Open File vs Select Folder#

  • Open File(s): select specific tiff files

  • Select Folder: load all supported files in folder

Load Options#

Option

Description

Separate ScanImage mROIs

split multi-ROI acquisitions

Enable Threading

parallel loading

Enable Data Preview Widget

full preview with window functions

Metadata Preview Only

show only metadata

Preview Widget#

Window Functions#

Function

Description

mean

average intensity over window

max

maximum intensity projection

std

standard deviation

mean-sub

mean-subtracted (highlights changes)

Parameters:

  • Window Size: frames to include (3-20 recommended)

  • sigma: spatial gaussian filter

Scan-Phase Correction#

Preview bidirectional phase correction before saving.

Parameter

Description

Fix Phase

enable/disable correction

Sub-Pixel

FFT-based sub-pixel correction

Upsample

sub-pixel precision (1/N pixel)

Exclude border-px

exclude edge pixels

max-offset

limit allowed offset

Workflow:

  1. view mean-subtracted projection (window 3-15)

  2. toggle Fix Phase on/off to compare

  3. adjust border-px and max-offset

  4. toggle Sub-Pixel for improvement

  5. adjust Upsample if needed (2-3 typical)

Summary Stats#

Per z-plane statistics (computed on every 10th frame):

Metric

Description

Mean

average intensity

Std

standard deviation

SNR

signal-to-noise (mean/std)

Saving Data#

Access via File → Save As or Process tab.

Output Formats#

Format

Description

.zarr

recommended for large data

.tiff

bigtiff

.bin

suite2p binary format

.h5

hdf5

Save Options#

Option

Description

Save mROI Separately

separate file per mROI

Overwrite

replace existing files

Register Z-Planes

suite3d axial registration

Fix Scan Phase

apply phase correction

Subpixel Phase Correction

FFT-based correction

Chunk Size (MB)

memory chunk size

Suite2p Processing#

Access via Process tab.

  • run suite2p on selected z-plane

  • all parameters exposed with descriptions

  • crop selector for spatial subset

Spatial Crop#

  1. click “Add Crop Selector”

  2. drag yellow rectangle on image

  3. only cropped region is processed

Python API#

from mbo_utilities.gui import run_gui

# from file
run_gui("/path/to/data")

# from numpy array
import numpy as np
data = np.random.rand(100, 512, 512)
run_gui(data)

If no input provided and Qt available, opens file dialog.

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