Software Installation
Computer Specifications
Below are the recommended specifications for navigate.
Operating System Compatibility
Important
navigate is developed for use on Windows-based systems. This is due to the compatibility of device drivers for various microscope hardware components, such as cameras, stages, and data acquisition cards, which are predominantly designed for the Windows environment. The software is only partially tested on MacOS and Linux systems. Users considering the use of navigate software on Linux should proceed with caution and be prepared for potential compatibility issues. For optimal performance and compatibility, it is strongly recommended to run navigate on a Windows machine.
Computer Considerations
navigate will run on a mid-range laptop with at least 8 GB of RAM and a processor with two cores. Most of its operations are undemanding. Saving data at a reasonable rate, however, will require an SSD. The hardware configuration for an example microscope control machine is shown below.
Important
Scientific cameras are capable of rapidly generating large amounts of high-resolution data. As such, the read/write speed of the data storage device is critical for smooth operation of the software. For example, for a standard Hamamatsu camera with a 2048 x 2048 sensor, operating at 16-bit depth and 20 frames per second, the data save rate is approximately ~167 MB/s. While such capabilities are well within the capabilities of modern SSDs, they are beyond the capabilities of most HDDs. Therefore, it is recommended to use a fast SSD for data saving operations.
Example Computer Configuration
- Base Platform
Product Name: Colfax SX6300 Workstation
Colfax Part #: CX-116263
- Primary and Secondary CPU
CPU Model: Intel Xeon Silver 4215R
Configuration: 8 Cores / 16 Threads
Frequency: 3.2 GHz
Cache: 11 MB
TDP: 130W
Memory Support: 2400 MHz
- Memory
Type: Registered ECC DDR4
Speed: 3200 MHz
Configuration: 16 GB per socket, 8 sockets per CPU
Total RAM: >64 GB (recommended)
- Operating System Drive:
Type: M.2 NVMe SSD
Model: Micron 7450 Max
Capacity: 800 GB
Endurance: 3 DWPD
- Primary Data Drive:
Type: NVMe SSD
Model: Samsung PM9A3
Capacity: 7.68 TB
Interface: U.2 Gen4
- Secondary Data Drive:
Type: SATA HDD
Model: Seagate Exos X20
Capacity: 20 TB
Speed: 7200 RPM
Cache: 256 MB
Interface: SATA 6.0 Gb/s
- Video Card
Model: PNY nVidia T1000
Memory: 4 GB
Interface: PCI Express
- Network Interface
Model: Intel X710-T2L RJ45 Copper
Type: Dual Port 10GbE
Interface: PCI-E x 8
Note
The specifications listed are based on an example system configuration and can be adjusted based on specific needs and availability.
Quick install
Setup your Python Environment
Head over to the miniconda website and install the appropriate version based on your operating system.
Tip
It is also handy to have the conda cheatsheet open when first using miniconda to get accustomed to the commands available.
Windows: Use the Windows taskbar search to find
Anaconda Prompt (Miniconda3). Given how frequently you will use this, we recommend pinning it to your taskbar. * Linux/Mac: Open a Terminal.
Create a Python environment called navigate that uses Python version 3.9.7
(base) MyComputer ~ $ conda create -n navigate python=3.9.7
Activate the navigate environment
(base) MyComputer ~ $ conda activate navigate
The active environment is shown in parentheses on the far-left. Originally, we were in the miniconda (base) environment. After activating the navigate environment, it should now show (navigate).
Install navigate via pip
To install the latest stable release of navigate, run the following command:
(navigate) MyComputer ~ $ pip install navigate-micro
To install the bleeding edge version of navigate, run the following command:
(navigate) MyComputer ~ $ pip install git+https://github.com/TheDeanLab/navigate.git
Run navigate software
(navigate) MyComputer ~ $ navigate
Note
If you are running the software on a computer that is not connected to microscope hardware, you can add the flag -sh (--synthetic-hardware) to launch the program:
navigate -sh