2021 Image Analysis Program
The 2021 Image Analysis Program is a series of tutorials and workshops aimed at microscopists of all skill levels using freely available tools such as Fiji and Python. No prior programming experience required.
This program has concluded. For recordings and more information on past workshops please see the links below or visit our Blog.
1. A Practical Guide to Mapping Brain Activity with ClearMap2
Tuesday, September 21, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Some of the key takeaways from this tutorial will be:
Considerations and parameters for imaging cFos and activity markers on the light sheet microscope at ZI
How to troubleshoot Python scripts and pipelines
How to use ClearMap2 for registration of whole-brain data and activity mapping
2. Whole brain reconstruction and analysis with BrainJ
Thursday, September 30, 2021 - 2:00 PM 4:00 PM with Luke Hammond -
Learn how to install and use BrainRender and Napari from your own computer. Working with example datasets this workshop will cover how to annotate and explore whole brain datasets obtained from BrainJ and ClearMap and how to efficiently create renderings for publications and presentations.
Some of the key takeaways from this tutorial will be:
How to automatically reconstruct and register whole brains and tissue volumes from data acquired from slide scanners and confocals.
How to automatically align these datasets to both the Allen Brain Atlas and the Unified Atlas (Kim et al. 2019).
How to map cells within a CCF using a variety of detection methods. Including machine learning segmentation with Ilastik.
How to perform mesoscale mapping of axons and dendrites within a CCF.
How to view and measure probe / GRIN lens placement or lesion and injection volumes within a CCF.
3. Visualizing whole brain data
Tuesday, October 5, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Learn how to use BrainRender and Napari to annotate and explore whole brain datasets from your own computer.
Some of the key takeaways from this workshop will be:
Using BrainRender for creating images and movies for publications and presentations.
Visualizing and isolating cell data from ClearMap or BrainJ in 3D renderings within Common Coorindate Frameworks (CCF) like the Allen Brain Atlas.
Visualizing raw data and axons/dendrites within CCFs .
Visualizing imaging regions or probe placements.
4. Cellular Imaging at Zuckerman Institute
Tuesday, October 19, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Learn about all the instruments and software tools available in the Cellular Imaging platform at the Zuckerman Institute to enable research.
From custom pipelines to specialized objectives and approaches that could save you time, help you avoid difficulties imaging and analyzing data, and open new doors to discovery.
5. Introduction to Fiji
Tuesday, October26, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Learn essential tools in Fiji/ImageJ for exploring and analyzing image data.
This tutorial will cover techniques for opening and working with multi-channel and 3D datasets including making measurements, understanding intensity, and performing image processing and segmentation.
Ideal for those new to image analysis and with limited experience using ImageJ, but we also cover less known features and time-saving shortcuts useful for even experienced microscopists.
6. Automating analysis with Fiji
Thursday, November 4, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Learn to automate image processing with macros and additional plugins for Fiji.
In this tutorial, we will focus on creating automated image processing pipelines with Fiji including 3D object segmentation, measuring intensity, and analyzing distance relationships. We will also cover additional plugins that extend the capability of Fiji for biomedical image analysis.
7. Automating machine learning segmentation and restoration in ImageJ / Fiji
Thursday, November 11, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Learn how to use Ilastik and StarDist for pixel and object classification, and how to use these powerful tools in an automated analysis pipeline in Fiji.
8. Automating Imaging and Analysis in NIS-Elements
Thursday, December 9, 2021 - 2:00 PM 4:00 PM with Luke Hammond
Advanced capabilities of NIS-Elements: Learn how to use JOBS, General Analysis, and deep learning segmentation to accelerate your research and automate imaging and analysis at the microscope.