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maikherbig authored Jul 26, 2022
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Expand Up @@ -2,18 +2,20 @@ This tutorial shows how to convert .cif files from ImageStream to .rtdc files an
how to use AIDeveloper and YouLabel to create a dataset and train a CNN model.
Here are the steps:

1. Install Java and Python environment for converting cif files (see [below instructions](#install-java-and-python-environment))
2. Download [YouLabel](https://github.com/maikherbig/YouLabel/releases)
3. Download [AIDeveloper](https://github.com/maikherbig/AIDeveloper/releases) and install update (see video)
4. Use a [Python script](https://github.com/maikherbig/AIDeveloper/blob/master/Tutorial%20ImageStream/cif_to_rtdc_v06.py) to convert .cif to .rtdc (see video)
1. Install Java (see [below instructions](#install-java))
2. Install Python environment for converting cif files (see [below instructions](#install-python-environment))
3. Download [YouLabel](https://github.com/maikherbig/YouLabel/releases)
4. Download [AIDeveloper](https://github.com/maikherbig/AIDeveloper/releases) and install update (see video)
5. Use a [Python script](https://github.com/maikherbig/AIDeveloper/blob/master/Tutorial%20ImageStream/cif_to_rtdc_v06.py) to convert .cif to .rtdc (see video)
6. Annotate data using [YouLabel](https://github.com/maikherbig/YouLabel/releases) (see video)
7. Use AIDeveloper to train CNN using Multi-Channel information (see video)
8. Use AIDeveloper to apply model to new data (see video)
9. Filter the data using probabilities, returned by the model (see video)


# Install Java and Python environment
# Install Java
First, install Java development kit (JDK). Windows installers can be obtained [on this website](https://www.oracle.com/java/technologies/downloads/#jdk18-windows), or via this [download link](https://download.oracle.com/java/18/latest/jdk-18_windows-x64_bin.exe).
# Install Python environment
Next, a Python distribution is required. I like to work with [miniconda](https://docs.conda.io/en/latest/miniconda.html).
Using conda, create a Python environment using following commands:
```
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