KINTSUGI: Knowledge Integration with New Technologies for Simplified User-Guided Image processing

Multiplex image processing for challenging datasets with a focus on user integration rather than automation. This pipeline includes 2D/3D GPU/CPU illumination correction, stitching, deconvolution, extended depth of focus, registration, autofluorescence removal, segmentation, clustering, and spatial analysis.

To view notebooks in browser see: https://smith6jt-cop.github.io/KINTSUGI-docs/Intro.html

Table of Contents

• Installation Steps
  • 1. Download miniforge
  • 2. Create mamba environment
  • 3. Download files
  • 4. Copy/move raw image data
• Notebooks
  • 1. Parameter tuning/testing
  • 2. Batch processing
  • 3. Signal Isolation
  • 4. Segmentation

Installation Steps

1. Download miniforge

 Download and install conda-based environment management software. If you already have, skip to step 2.

 Download miniforge: https://github.com/conda-forge/miniforge.

 Follow installation instructions for your OS.

2. Create mamba environment

 Launch miniforge as administrator (if possible). You will be in the default “base” environment.

 Change directory to your user folder:

cd C:\Users\[your user name]

 To download the code and associated files enter:

git clone https://github.com/smith6jt-cop/KINTSUGI.git

 Change directory to enter the folder just downloaded

cd KINTSUGI

 Create the environment by entering:

mamba env create -f environment.yml

 Activate the environment by entering:

mamba activate KINTSUGI

 It is recommended to use VS Code to run the notebooks. Download and install VS Code [https://code.visualstudio.com/](https://code.visualstudio.com/).


#### 3. Download dependency files
 Download zip files and extract them to KINTSUGI folder. 

#### 4. Copy/move raw image data  
 Create a folder in the KINTSUGI folder called “data”.  

 If downloading test data use this link: [https://uflorida-my.sharepoint.com/:f:/g/personal/smith6jt_ufl_edu1/Er5ui-wFA6BNnmgj9N1hPAsBYQaiKfSQa2do_lUMhQdaGg?e=5Uny95](https://uflorida-my.sharepoint.com/:f:/g/personal/smith6jt_ufl_edu1/Er5ui-wFA6BNnmgj9N1hPAsB_Z8EwL7jkfekJwrWEfVRbw?e=oxaxMH)  

 Move all image data to [your user folder]\KINTSUGI\data.  


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## Notebooks
[1. Parameter tuning/testing](notebooks/1_Single_Channel_Eval.ipynb)
  For testing illumination correction, stitching, deconvolution, and EDoF.

[2. Batch processing](notebooks/2_Cycle_Processing.ipynb)
  For batch processing illumination correction, stitching, deconvolution, EDoF, and registration.

[3. Signal Isolation](notebooks/3_Signal_Isolation.ipynb)
  For autofluorescence subtraction, filtering, and final processing to isolate signal.

[4. Segmentation](notebooks/4_Segmentation.ipynb)
  For Mesmer segmentation and feature extraction.

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