Running CellTracksColab using Google Colab

Video Tutorials

If you are unfamiliar with Google Colab, you can watch the following tutorials to get started:

Colab 101: Your Ultimate Beginner's Guide!

Using CellTracksColab with Google Colab

To Get Started You Need

• A Google account
• Upload your tracking data to Google Drive
• Ensure your data is properly organized according to our data requirements and supported software

Open the Notebook You Want to Use

You can access the notebooks directly from here.

Open the Notebook: Click on the open in colab button.

While you can use the notebooks directly, we recommend that you first save the notebook in your own Google Drive. Here’s how you can do it:

Save to Google Drive: - Once the notebook is open in Google Colab, go to the top menu and click on File. - From the dropdown menu, select Save a copy in Drive. - A new tab will open with a copy of the notebook saved to your Google Drive.

This way, you can easily access and edit the notebook.

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Prepare the Session and Load Your Data

Once you have opened the notebook you want to use, follow the instructions and run the code cells in sequence, one after the other, to ensure smooth execution.

1. Installation and Setup

• Set up the necessary dependencies and libraries.
• Install the required packages.
• When running the notebook locally, this step can be skipped.

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2. Setting Up Your Google Drive Connection

• Ensure your data is available on Google Drive.
• Authenticate and authorize the notebook to access your Google Drive.

• Click on the Files tab on the left sidebar in Google Colab to see if you have successfully connected to your Google Drive. You should see your Google Drive folder in the left menu.

• If you cannot see your Google Drive, you need to reconnect to the hosted runtime by clicking the small arrow at the top right of the page.

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3. Load the Key Dependencies

• Load the installed dependencies.

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4. Navigating to Your Dataset on Google Drive

1. Access Google Drive within Colab:

   • Click on the Files tab on the left sidebar in Google Colab to access your Google Drive files.

2. Locate Your Dataset:

   • Browse and find the folder that contains your dataset.

3. Specify a Dataset Folder:

   • Ensure the Folder_path parameter in the notebook reflects the exact path to your tracking dataset on Google Drive.
   • Tip - to quickly insert the tracking folder path, right-click on the desired folder and click copy-path and paste it to the Folder_path cell.

4. Adhere to Data Organization:

   • Please make sure your data is organized as required. The data requirements might vary depending on which notebook you're working with.
     • For the General notebook: Data Organization & Requirements
     • For the TrackMate notebook: Data Organization & Requirements

5. Using the Test Dataset (Optional):

   • To explore using the provided test dataset, tick the Use_test_dataset box.
   • This will prompt the notebook to download and load the test dataset for you automatically.

6. Specify a Results Folder:

   • Choose a directory on your Google Drive for storing analysis results.
   • Adjust the Results_Folder parameter to match your chosen path.

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