🔬 RAMFISH Studio

RAMFISH Studio brings the five tools of the RAMFISH Software Suite together in one app that opens in your web browser:

1. Import & normalize → 2. Rough alignment → 3. Fine alignment → 4. Spot counter → 5. Multiplex merge

Everything runs on your own computer. Your images are never uploaded anywhere.

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🌱 Installation (one time only)

Step 1: Install Miniconda

Download and install Miniconda for your operating system from the official documentation:

• Windows: Install the Python 3.12 64-bit Miniconda installer. During installation, select Just Me. Adding Miniconda to PATH is optional; using the Miniconda Prompt is recommended.
• Linux (x86_64): Run:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -f ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash

• macOS Apple Silicon (M1/M2/M3/M4): Install the MacOSX-arm64 Miniconda package.
• macOS Intel: Install the MacOSX-x86_64 Miniconda package.

Official Miniconda documentation:

https://docs.conda.io/en/latest/

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Step 2: Create the RAMFISH Environment

Open Anaconda Prompt / Miniconda Prompt on Windows, or a terminal on macOS/Linux.

Run the following commands one at a time:

1. Create the environment

conda create -n ramfish python=3.12 -y

2. Activate the environment

conda activate ramfish

3. Install Java and Bio-Formats support

conda install -c conda-forge bioformats_jar openjdk maven -y

4. Install the app dependencies

pip install streamlit pandas numpy scipy scikit-image tifffile imagecodecs imageio opencv-python SimpleITK pillow "aicsimageio>=4.14,<5" "numcodecs<0.16.0" scyjava

5. Optional: Install NVIDIA GPU acceleration

For NVIDIA GPUs supporting CUDA 12.x:

pip install "cupy-cuda12x[ctk]"

For systems using CUDA 11.x, use:

pip install "cupy-cuda11x[ctk]"

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Step 3: Download RAMFISH Studio

On this GitHub page, click the green Code button → Download ZIP, unzip it into your Documents folder and rename the unzipped folder to RAMFISH_Studio.

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🚀 Start RAMFISH Studio (every time)

Open Anaconda Prompt / Miniconda Prompt on Windows, or a terminal on macOS/Linux, and run:

1. Activate the environment

conda activate ramfish

2. Go to the RAMFISH Studio folder

cd Documents/RAMFISH_Studio

3. Start the app

streamlit run app.py

The app opens in your web browser. Keep the prompt/terminal window open while you work; close it when you are done.

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🧬 Using the app

Work through the five steps in the left menu. Each page tells you exactly what to do.

1. Import & normalize: type a project name and load your images, one folder per round (Round_1, Round_2, …). Name the nuclear stain DAPI (or the tissue outline mask) and every other image after its gene.
2. Rough alignment: drag the sliders until each round overlaps Round 1, then click Apply Rough Alignment to Round.
3. Fine alignment: click Run Batch Alignment.
4. Spot counter: click Run spot counter to count the mRNA spots of every gene.
5. Multiplex merge: pick colors and click Generate Composite.

All results are saved in the Output folder inside the RAMFISH Studio folder:

Output/<project name>/
├── 1_normalized/
├── 2_rough_aligned/
├── 3_fine_aligned/
├── 4_spots/
└── 5_merge/

For a quick test you can run the online version with the two round example datasets provided along with this repository: https://ramfishstudio.streamlit.app/

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💻 Hardware Requirements

Component	Recommended	High Performance
CPU	AMD Ryzen 5 5600X / Intel Core i5-12400F	AMD Ryzen Threadripper 9965WX
GPU	NVIDIA RTX 3060	NVIDIA RTX 5080 / RTX 5090
RAM	32 GB DDR4	128 GB DDR5
Storage	SSD recommended	High-speed NVMe SSD

Tested on Windows 11 and Ubuntu 24.04.

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License

MIT License, © 2026 Tirtha Das Banerjee