Online
Mar 1, 2021
9:00 am - 12:00 pm
Instructors: Erick Ratamero, Dave Mellert, Eric Perlman
Helpers: Sue McClatchy
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In this short workshop, we will present the existing ways to write Python code to interact with an OMERO server. This allows for programmatic access to image pixels and metadata related to images stored in the OMERO platform. Students should be comfortable with basic Python and interested in writing code to automate image analysis and/or data management.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Mar 1, 2021. Add to your Google Calendar.
Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email susan.mcclatchy@jax.org or erick.ratamero@jax.org for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Please be sure to complete this survey after the workshop.
| 09:00 | Introduction |
| 09:15 | Introductory example: retrieving an image from OMERO using two different APIs |
| 09:45 | The JSON API: interacting with OMERO.web |
| 10:20 | Morning break |
| 10:35 | The Blitz API: interacting directly with the OMERO server |
| 11:30 | Future directions: zarr, NGFF, working with large datasets |
| 12:00 | END |
To participate in a workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
If you haven't used Webex before, please ask the IT help desk to download and install the client for your computer.
Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:
Please connect to Global Protect VPN if you’ve never done so. Questions? Please contact the IT help desk at 207 288 1414.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
yes and press enter to approve the license.
Press Enter (or Return)
to approve the default location
for the files.
Type yes and press
Enter (or Return)
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).