QCima Studio

Standalone quality-control software for MACSima® spatial proteomics datasets

Field	Information
Version	1.0.0 — July 2026
Author / developer	Dr. Daniel Peter Varga
Organization	Image and Data Analysis Facility (IDAF), German Center for Neurodegenerative Diseases (DZNE), Bonn
DOI	10.5281/zenodo.21235383
Platform	Windows 10/11, 64-bit
Implementation	MATLAB; compiled standalone application with MATLAB Runtime
Distribution	Free research use under the accompanying closed-source software licence
Contact	idaf@dzne.de

Summary

QCima Studio is a standalone application for structured visual quality control of multiplexed images generated by the MACSima spatial proteomics platform. It was developed at IDAF, DZNE Bonn, to address a recurring bottleneck: reviewing large numbers of antibody signals together with their background, autofluorescence and DAPI reference images across multiple regions of interest and acquisition cycles.

The application consolidates this process into one interface. Users navigate through ROIs and antibody channels, adjust visualization, inspect overlays, document observations and classify channels as Keep or Discard. Projects can be resumed and classifications exported to MACS iQ View. Original image data are never modified.

Problem addressed

MACSima experiments can contain hundreds of related image files distributed across cycles, channels and ROIs. Conventional QC requires users to locate and compare these files manually, often using several applications or custom scripts. This is time-consuming, difficult to standardize and dependent on experienced operators.

QCima Studio was designed to:

• reduce the effort required for signal-level QC;
• make QC accessible without programming;
• improve consistency and traceability of decisions;
• support large, multi-ROI datasets efficiently;
• connect visual QC with downstream MACSima analysis;
• provide a documented workflow for research groups and core facilities.

Main functionality

Data loading and organization

The software loads the standard MACSima project structure and requires the corresponding RawData and PreprocessedData folders. It validates the dataset and parses file names and metadata to identify rack, well, ROI, imaging cycle, antibody, background, autofluorescence and DAPI information.

Projects containing multiple ROIs and large antibody panels are organized into a consistent internal representation. Antibodies acquired with several fluorophores are temporarily distinguished as AB-I, AB-II, AB-III, etc.; original names are restored during export.

Interactive QC workflow

The graphical interface provides:

• ROI and signal selection;
• rapid navigation through antibody images;
• brightness and contrast adjustment;
• autofluorescence, background and DAPI overlays;
• magnification and rectangular zoom;
• multiresolution viewing;
• signal-specific comments;
• Keep and Discard classification;
• keyboard shortcuts for common controls.

Displaying antibody signals together with their references helps users distinguish genuine staining from background, autofluorescence, acquisition artefacts or otherwise unsuitable signals.

Efficient image handling

QCima Studio uses on-demand loading and caching instead of loading an entire experiment into memory. Pyramidal TIFF files are accessed through TIFF SubIFD indexing so that only the required resolution level is read.

Saving, reporting and export

QC projects can be saved and reopened with their classifications, comments and visualization settings. Temporary graphical handles are excluded from saved project structures, keeping session files compact.

Available outputs include:

• saved QC project sessions;
• PNG export of the current image view;
• overview tables;
• antibody-panel exports;
• DAPI-cycle overview exports;
• MACS iQ View-compatible channel settings.

The DAPI-cycle report displays DAPI images across all cycles for a selected ROI and plots mean DAPI intensity over the complete field of view. It can reveal progressive photobleaching, DAPI restaining events and possible stitching inconsistencies, including XY-size differences relative to the first cycle.

MACS iQ View integration

The software exports .qiChannelSettings files and can assign the DoNotAnalyse flag to discarded channels. This transfers QC decisions to the downstream workflow without modifying source images.

Technical design

QCima Studio was developed in MATLAB as a modular desktop application and compiled for 64-bit Windows. End users do not require a MATLAB licence; the application uses the corresponding MATLAB Runtime.

Documentation and test data

The release includes a user guide covering installation, system requirements, supported data structures, loading and validation, interface controls, the recommended QC workflow, saving, reporting, MACS iQ View transfer, troubleshooting, known limitations and version history.

A curated test dataset supports installation checks and training. It is based on LAT_EXP0003_2025-09-29_08-02-07 and contains two ROIs and a reduced antibody subset.

Release and governance

QCima Studio v1.0.0 is distributed as a standalone installer with documentation, licence information, test-data instructions. Institutional Nextcloud is used for distribution, while the Zenodo DOI provides a persistent citation endpoint.

The source code remains closed, while the compiled software is available free of charge for research use under the accompanying software licence agreement.

Scientific and operational value

QCima Studio translates expertise in microscopy, image analysis and spatial proteomics into reusable research software. Its main contributions are:

1. Reproducibility: classifications, comments and settings are stored with the project.
2. Usability: researchers can perform structured image QC without scripts.
3. Efficiency: multiresolution access and caching support large datasets and multiple ROIs.
4. Interoperability: QC decisions can be transferred to MACS iQ View while source data remain untouched.
5. Facility applicability: one workflow can be used across projects, operators and collaborating groups.
6. Transparency: documentation, known limitations, versioning, checksums and persistent citation support responsible distribution.
7. Research impact: exclusion of unsuitable channels improves the reliability of downstream segmentation, clustering and spatial analysis.

The software is particularly relevant to imaging and spatial-omics core facilities, where consistent procedures, traceable decisions and efficient support of many users are essential.

Limitations and outlook

Version 1.0.0 is specifically designed for MACSima data structures and is not yet a platform-independent spatial-proteomics viewer. Compatibility depends on the expected folder, filename and metadata conventions.

Potential future developments include:

• modular import support for additional imaging platforms;
• expanded quantitative QC metrics;
• automated stitching and illumination-consistency assessment;
• institutional or DOI-linked update checking;
• compatibility testing with future MACSima and MATLAB Runtime versions.

QCima Studio is maintained through IDAF at DZNE Bonn. Version control, documented releases, a persistent DOI and representative test data support continued maintenance.

Recommended citation

Varga, D. P. (2026). QCima Studio (Version 1.0.0) [Computer software]. Image and Data Analysis Facility, German Center for Neurodegenerative Diseases (DZNE), Bonn. https://doi.org/10.5281/zenodo.21235383