MIST4Cores stitcher

An easy-to-use application for automating the stitching of sequential images for dendrochronological samples.

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Installation

In the Releases section of this repository, you will find the executable file mist4cores-stitcher.exe

Once downloaded, open the program and follow the next steps:

Recomended: place the downloaded file in a new folder

Note: You must have Fiji installed beforehand, and also the plugin MIST (see MIST Project)

Initial Setup

1. Locate Fiji Installation:
   Specify the directory where Fiji.app is located

2. Set the Monitoring Directory:
   Select the directory to be monitored for existing or new folders containing images. This directory may include a set of subfolders, each holding its own collection of images.

3. Select Output Directory:

   • Choose same directory to save the stitched image in the same directory as the original images
   • Choose custom directory to select a custom output directory where all stitched images will be saved

4. Choose JVM memory size:

   • By default, the JVM memory size is set to 8 GB , but this value can be adjusted based on your system's available resources.
   • If your machine has 16 GB of RAM , it is often advisable to allocate a smaller portion of memory to the JVM, such as 8 GB.

5. Output Format:

   • Select the desired format for the stitched image: .ome.tif, .tif, or both.

6. Start Monitoring:
   After completing the configuration, you can choose between two options for stitching images:

   • Process Existing Folders: When the Save Mode button is pressed, the program will stitch all existing folders containing images, skipping those that have already been stitched (indicated by the presence of .ome.tif files)
   • Monitor Future Folders: The program will actively monitor new folders with images as they are added, ignoring any folders that already exist at the time this option is activated

   To stop monitoring and close the program, there is a button below (Stop)

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Configuration

MIST4Cores Parameters:
The config.json file contains the callable MIST stitching parameters, which can be modified directly within the file. This file is located in the same directory as the mist4cores-stitcher.exe executable.

Parameters accessed via config.get will use the saved configuration values. Other parameters are dynamically calculated at runtime

Image Pattern:
The program uses the following regular expression to match image file names:

  ([a-zA-Z0-9]+)_(\d+)\.(\w+)

Files must have a prefix followed by an underscore _ and two digits, ending with the file extension

Example: vVLQPy15_01.jpg

• MIST accepts the pattern defined as: prefix_{pp}.jpg

If you want to modify the pattern, you can do so by editing the conf.json file under the pattern key

Note: If the images do not match the defined pattern, the folder will be discarded and the program will move on to the next one.

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Images Extensions

The program will process the folder for images with the following extensions:
.png, .jpg, .jpeg, and .tif

Information About Stitched Images

Each stitched image has an associated file (_info.txt) that contains details such as the sample name, stitching date, number of images stitched, horizontal and vertical overlap percentages, the input directory, the output directory, and the version of ImageJ used.

Libraries

The requirements.txt file lists the external libraries required to run the program. It is located in the same directory as the config.json file.

Log Summary

In the Monitor Directory you will find a file named stitching_summary_log.txt which contains the summary of the stitching process for all processed directories.

• Date and Time of Execution

• Directory

• Status:

  • "Successful stitching"
  • "Failed (Not all images selected)"
  • "Failed (Stitching image not saved)": usually because an Out Of Memory exception is raised
  • "Failed"

• Time Elapsed (seconds)

• Images Processed

  Note: revise that the total number of images is correct. Not all images in a directory may be selected for stitching, even if the process completes successfully

• Output Image Size (KB)

How to cite

In case you use MIST4Cores, please use the following reference: García-Hidalgo M., Ye Y., García-Pedrero Á., Olano JM. (2025). Mist4Cores: Reliable batch image stitching for dendrochronological cores. (Preprint) doi: https://doi.org/10.1101/2025.10.17.667188

References

Chalfoun, J., Majurski, M., Blattner, T. et al. (2017). MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization. Sci Rep 7, 4988. https://doi.org/10.1038/s41598-017-04567-y Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, … Cardona A (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods 9: 676–682. doi:10.1038/nmeth.2019