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**NOTE**: For M1/M2 Macs, which use the ARM 64-bit architecture, use [this link](https://www.azul.com/downloads/?version=java-11-lts&os=macos&architecture=arm-64-bit&package=jdk) to get Java 11.
For beginners, we recommend you use Anaconda Navigator since it is more beginner-friendly. Download Anaconda from the website [here](https://www.anaconda.com/products/distribution), then open Anaconda Navigator
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2.**Download and install or update conda**
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For beginners, we recommend you use Anaconda Navigator since it is more beginner-friendly, but you can also use miniconda. [Download Anaconda](https://www.anaconda.com/products/distribution) from the website and install.
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3. Download the environment file
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**NOTE**: if you already have conda, you can get the command to update conda by typing `conda update` on your command line. The command will generally look like:
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You can download the whole repo by cloning it with git or simply clicking the green **Code** button on [the repo page](https://github.com/CellProfiler/CellProfiler-plugins.git) and selecting **Download ZIP** (see below) and then extract the ZIP folder contents.
Alternatively, you can copy and paste the contents of the .yml file into a text editor like Notepad. If you do this, make sure you save it as "CellProfiler_plugins_windows.yml" and as type "All Files" and **NOT** "Text file".
Download a copy of (aka "clone") the CellProfiler-plugins repo from [here](https://github.com/CellProfiler/CellProfiler-plugins.git). You can download the whole repo by cloning it with git or simply clicking the green **Code** button on [the repo page](https://github.com/CellProfiler/CellProfiler-plugins.git) and selecting **Download ZIP** (see below).
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4. Try to create a new environment from the included .yml file
You can also use git or GitHub Desktop to clone the repo if you prefer.
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**Warning, this step may take a while**
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4.**Create the environment from the .yml file**
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Open Anaconda Navigator and select the **Environments** tab on the left. We recommend you create the environment from the command line. To do this, Select the play button next to your base (root) environment and select **Open Terminal**:
A black box should pop up with a blinking cursor. This is your terminal. You now need to navigate to where the **cellprofiler_plugins_mac.yml** file is inside of the CellProfiler-plugins folder you downloaded in the last step. This file is in the `Instructions` subfolder. Here is how we recommend you do this:
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1) In Finder, open the folder you downloaded in the previous step (usually called "CellProfiler-plugins-master")
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2) There should be a folder called **Instructions**. Right click or ctrl+click that folder. Then hold down the option key (or Alt) on your keyboard. An option to **Copy "Instructions" as Pathname** should appear. Select this option. (see below)
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In the terminal, navigate to where your environment file is located with `cd PATH_TO_FOLDER` where `PATH_TO_FOLDER` is the path to the directory containing your yml file (e.g., `/Users/USER/Desktop`).
Then in the terminal window that pops up, enter the following command:
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3) Go back to your terminal and type `cd PATH_TO_FOLDER` where `PATH_TO_FOLDER` is the address you copied in the previous step. Press Enter.
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Now that you're in the right place, copy and paste this command into the terminal and press Enter.
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```
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conda env create -f CellProfiler_plugins_mac.yml
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```
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5. Activate your environment
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In your terminal, enter `conda activate Cellprofiler_plugins` to activate your environment
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5.**Activate your environment**
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In your terminal, enter `conda activate CellProfiler_plugins` to activate your environment
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6. Verify that cellprofiler is installed correctly by running it from the command line.
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6.**Verify that cellprofiler is installed correctly by running it from the command line.**
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In your terminal, type in `pythonw -m cellprofiler` and hit Enter. this will open CellProfiler or will give you an error message.
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7. Install other packages for other plugins (just for RunStarDist)
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7.**Install other packages for other plugins**
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In terminal with your environment activated, enter:
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Certain packages cannot easily installed when importing the environment.
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For StarDist: In terminal with your environment activated, enter:
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```
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pip install stardist csbdeep --no-deps
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```
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If you would like to use the omnipose models in cellpose, ensure you have cellpose 1.0.2 (you should by default if you've used our environment yml) and enter on the command line (in your activated environment):
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If you would like to use the omnipose models in cellpose, ensure you have cellpose 1.0.2 (you should by default if you've used the CellProfiler_plugins_mac.yml file to generate the environment) and enter on the command line (in your activated environment):
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```
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pip install omnipose
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```
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8. Clone the CellProfiler-plugins Repo
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If you have not already downloaded the repo, download it from [here](https://github.com/CellProfiler/CellProfiler-plugins.git).
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You can also use git or GitHub Desktop to clone the repo if you prefer.
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9. Connect CellProfiler and the plugins repo
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8. **Connect CellProfiler and the plugins repo**
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With your environment active, type `pythonw -m cellprofiler` in terminal to open CellProfiler if it is not open already.
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* In CellProfiler, go to **File** then **Preferences...**
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* Scroll down and look for "CellProfiler Plugins Directory" on the left.
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* Select the **Browse** button and choose the folder where you extracted the CellProfiler plugins files. It is probably called "CellProfiler-plugins-master" unless you have renamed it.
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* Select **Save** at the bottom of the Preferences window
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* Close CellProfiler and reopen it by typing `pythonw -m cellprofiler` on the command line
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* In CellProfiler, go to **File** then **Preferences...**
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* Scroll down and look for "CellProfiler Plugins Directory" on the left.
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* Select the **Browse** button and choose the folder where you extracted the CellProfiler plugins files. It is probably called "CellProfiler-plugins-master" unless you have renamed it.
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* Select **Save** at the bottom of the Preferences window
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* Close CellProfiler and reopen it by typing `pythonw -m cellprofiler` on the command line
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**NOTE**: You might get a warning like this:
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```
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If you don't have a GPU, this is not a problem. If you do, your configuration is incorrect and you need to try reinstalling drivers and the correct version of CUDA for your system.
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10. Verify that the installation worked
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9. **Verify that the installation worked**
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Add a module to your pipeline by hitting the **+** button in the pipeline panel (bottom left)
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# How to install CellProfiler from source with all plugins on Windows
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Some of these download steps can take a while. The first 3 steps (as well as downloading Anaconda) can all be done simultaneously to save you time.
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Outlined here is the manual process for installing CellProfiler and plugins from source. Please close all open programs and save your work before starting this, as your computer may require a restart. Note that some of these download steps can take a while; the first 3 steps (as well as downloading Anaconda) can all be done simultaneously to save you time. Also note that for steps like changing the system-level environment variables, you may need admin permissions on your computer.
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1.**Download and install [Microsoft Visual Studio C++ build tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/)**
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**NEW:** We now have an automated install available for this workflow (requires administrator permissions on your computer) that will perform these steps for you. To get the necessary files and see instructions for the automatic install, look [here](https://github.com/CellProfiler/CellProfiler-plugins/tree/master/Instructions/Windows_batch_file).
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1.**Download and install [Microsoft Visual Studio C++ build tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/)**
2.**Download and install [Microsoft Visual C++ Redistributable 2015-2022](https://docs.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170)**
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3.**Download and install [Java JDK 11](https://adoptopenjdk.net/)**
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3.**Download and install [Java JDK 11](https://adoptium.net/temurin/releases/?version=11)**
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Make sure you select the right version for your processor and operating system (see previous step). You can filter by operating system and processor Architecture.
You can alternatively install from [oracle.com](https://www.oracle.com/java/technologies/javase-jdk11-downloads.html) if you'd like, though you will need to make an Oracle account.
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4.**Update your Windows Environment Variables for Java**
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Go to **Control Panel** then search for **System**, then click on **Advanced System Settings**
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Go to **Control Panel** then search for **System**, then click on **Advanced System Settings**. Alternatively, for some versions of Windows, you can use the search bar to search for "Environment" and "Edit the system environment variables" will come up as an option.
From the System Properties window that pops up, select **Environment Variables...** Then add a new System variable by selecting **New...** under 'System Variables':
Add (or if you already have it, modify) two system variables: `JAVA_HOME` and `JDK_HOME`. For each new variable, set its value to the location of your JDK installation (i.e., the location of the folder beginning with 'jdk11'). You can do this by clicking the **Browse Directory...** button. Usually this is in your 'Program Files' in a folder called 'Java'. Here is an example path:
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Add (or if you already have it, modify) two system variables: `JAVA_HOME` and `JDK_HOME`. For each new variable, set its value to the location of your JDK installation (i.e., the location of the folder beginning with 'jdk11'). You can do this by clicking the **Browse Directory...** button. Usually this is in your 'Program Files' in a folder called 'Java'. Here is an example path for `JAVA_HOME`:
For beginners, we recommend you use Anaconda Navigator since it is more beginner-friendly, but you can also use miniconda. [Download Anaconda](https://www.anaconda.com/products/distribution) from the website and install.
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6.**Download the environment file [CellProfiler_plugins_windows.yml](https://github.com/CellProfiler/CellProfiler-plugins/blob/master/Instructions/cellprofiler_plugins_windows.yml)**
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You can download the whole repo by cloning it with git or simply clicking the green **Code** button on [the repo page](https://github.com/CellProfiler/CellProfiler-plugins.git) and selecting **Download ZIP** (see below) and then extract the ZIP folder contents. The environment file is in the `Instructions` subfolder.
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6.**Clone the CellProfiler-plugins Repo**
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Alternatively, you can copy and paste the contents of the .yml file into a text editor like Notepad. If you do this, make sure you save it as "CellProfiler_plugins_windows.yml" and as type "All Files" and **NOT**"Text file".
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Download a copy of (aka "clone") the CellProfiler-plugins repo from [here](https://github.com/CellProfiler/CellProfiler-plugins.git). You can download the whole repo by cloning it with git or simply clicking the green **Code** button on [the repo page](https://github.com/CellProfiler/CellProfiler-plugins.git)and selecting **Download ZIP**(see below).
You can also use git or GitHub Desktop to clone the repo if you prefer.
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7.**Create the environment from the .yml file**
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Open Anaconda Navigator and select the **Environments** tab on the left. We recommend you create the environment from the command line. To do this, Select the play button next to your base (root) environment and select **Open Terminal**:
In the terminal, navigate to where your environment file is located with `cd PATH_TO_FOLDER` where `PATH_TO_FOLDER` is the path to the directory containing your yml file (e.g., `C:/Users/USER/Desktop`).
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Then in the terminal window that pops up, enter the following command:
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A black box should pop up with a blinking cursor. This is your terminal. You now need to navigate to where the **cellprofiler_plugins_windows.yml** file is inside of the CellProfiler-plugins folder you downloaded in the last step. This file is in the `Instructions` subfolder. Here is how we recommend you do this:
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1) In File Explorer, open the folder you downloaded in the previous step (usually called "CellProfiler-plugins-master") and then open the **Instructions** subfolder).
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2) Click in the address bar area and this should highlight an address to where the folder is on your computer. **Copy this address**:
In your terminal, enter `conda activate Cellprofiler_plugins` to activate your environment
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In your terminal, enter `conda activate CP_plugins` to activate your environment
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9.**Verify that cellprofiler is installed correctly by running it from the command line.**
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In your terminal, type in `cellprofiler` and hit Enter. this will open CellProfiler or will give you an error message.
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10.**Install other packages for other plugins (just for RunStarDist)**
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In terminal with your environment activated, enter:
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pip install omnipose
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```
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11. **Clone the CellProfiler-plugins Repo**
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If you have not already downloaded the repo, download it from [here](https://github.com/CellProfiler/CellProfiler-plugins.git). If you download the ZIP file, be sure to extract the file contents by selecting **Extract All** in File Explorer:
You can also use git or GitHub Desktop to clone the repo if you prefer.
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12. **Connect CellProfiler and the plugins repo**
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12. **Connect CellProfiler and the plugins folder**
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With your environment active, type `cellprofiler` in terminal to open CellProfiler if it is not open already.
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```
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If you don't have a GPU, this is not a problem. If you do, your configuration is incorrect and you need to try reinstalling drivers and the correct version of CUDA for your system.
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13. **Verify that the installation worked**
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Add a module to your pipeline by hitting the **+** button in the pipeline panel (bottom left)
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