Set-up and Installation

Before you can run the kelp-o-matic tool, you will need to set up some programs which will allow the tool to run. Once set-up is complete the tool can be run very easily from ones terminal.

Install Anaconda

If not already installed, download Anaconda on your computer from the Anaconda download website. Follow the prompts to install the most recent version of Anaconda for your operating system.

Install Anaconda

Create New Environment

Open Anaconda

Once Anaconda is installed, open Anaconda Navigator by typing “Anaconda Navigator” in the start menu.

Click on "Environments"

In the tab on the left, click on Environments.

Click "Create" to make a new environment

Create a new environment and give it a name by clicking the create button.

Type name and click "create"

Give the new environment a name in the dialogue box that pops up, e.g. "KelpSegmentation". Select a Python version that begins with "3.9".

Warning

kelp-o-matic currently supports Python versions 3.7, 3.8, 3.9, and 3.10. Installation will not work for other versions.

Add Channels

Click on "Channels"

With the new environment selected in the environment tab, click the channels button.

List of added channels

In the dialogue box that pops up click the “Add…” button.

Type name of channel to add

Add the channels "conda-forge" and "pytorch" by typing the name of each channel in the space and then click update channels.

Note

The "hakai-institute" channel, shown in the image, is no longer required. However, it won't cause any issues if you've added it already.

Warning

Watch your spelling! Anaconda won't be able to find the packages you need to install if the channel names are misspelled.

Update channels

Click "update channels".

Install Packages

Next you will install the kelp-o-matic package in your environment.

Select "not-installed"

In the Anaconda Navigator with your environment selected and “Not Installed” selected in the drop down menu, type “kelp-o-matic” in the search packages search bar.

Type "kelp-o-matic"

Type kelp-o-matic in the search packages search bar. This is the name of the package you are installing (make sure it is spelled correctly).

Select "kelp-o-matic" package

Click the box beside kelp-o-matic and then click Apply to install the package.

Click "apply"

A dialogue box will appear and ask you to install packages, click the apply button.

"kelp-o-matic" appears in installed

Now when you select Installed on the drop-down menu the kelp-o-matic package should appear.

Part 1 set-up is now complete!

You are now ready to run the Kelp-O-Matic tool. Now that the setup steps are completed, you will not have to repeat them again unless installing on a different computer.

Authors: Sarah Schroeder and Taylor Denouden