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Cropping Olympus CellSense MIA to ROI

02 Jul 11:48
@JulBaer JulBaer
v1.0
8567746
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Cropping Olympus CellSense MIA to ROI Latest
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Release Notes

crop_OlympusCellSense_MIA.m

Overview

This release publishes crop_OlympusCellSense_MIA.m, a MATLAB script designed to help users efficiently process large Olympus CellSense MIA stitched microscopy images. The script enables users to define image sets, interactively select regions of interest (ROIs), and export each ROI as a series of single-page TIFF files (one per timepoint and imaging channel). It also supports automated export of timelapse movies for each ROI.

Features

  • Interactive ROI Selection:
    Users can visually select and name multiple ROIs per image or image row. For very large images, the script allows pre-splitting images into horizontal rows before ROI selection, making interactive cropping feasible even for images that exceed system RAM.

  • Batch Processing:
    Multiple image sets can be defined and processed in a single run, using a cell array of parameter structs. This streamlines high-throughput workflows.

  • Export Options:

    • Cropped ROIs are saved as single-page TIFF files.
    • Optionally, each ROI is exported as a timelapse movie (AVI format) combining all timepoints and channels.

  • Multi-Channel Support:
    Any number of imaging channels is supported. Each channel is handled individually, and channel-specific color mapping can be set for movie export. Only tested for 1 to 3 channels!

  • Robust to Large File Sizes:
    Handles images larger than available RAM by reading and displaying only slices or subregions needed for ROI selection and cropping.

  • Customizable Parameters:
    All important settings (input directories, scaling, frame rate, bit depth, ROI splitting, etc.) are specified in a clear parameter section at the top of the script.

  • User Guidance:
    Script prompts guide the user through ROI selection, including naming and drawing each ROI.

Usage

  1. Edit the "USER IMAGE SET PARAMETERS" section of the script to specify the image sets you want to process.
  2. Run the script in MATLAB. You will be prompted to select and name ROIs for each specified image set and row.
  3. The script will save cropped TIFF images and movies for each ROI in organized output folders.

Notes

  • All TIFF images and movies are saved in subfolders within the specified main directory for each image set.
  • The script uses the Bio-Formats library for efficient image reading and supports multi-channel and multi-timepoint data.
  • Predefined channel colors and other visualization settings can be customized at the top of the script.

Limitations

  • Only single-page TIFF export is supported (no multipage TIFFs).
  • The script assumes Olympus CellSense MIA directory and file structure.
  • Manual interaction is required for ROI selection (no automated ROI detection).

If you encounter any issues or have suggestions for improvements, please open an issue on this repository.

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