Automating Imaging and Analysis in NIS-Elements

This tutorial covers using advanced features in Nikon's NIS-Elements software to enable advanced automation of imaging and analysis. We include step-by-step procedures that allow you to use Nikon instruments to their full potential. These include: - Using Jobs to automate imaging and perform on-the-fly analysis - reducing the time you need to spend at the microscope and increasing data collection. - Building analysis pipelines in General Analysis 3 to perform analysis in batch or during image acquisition. - Training and using deep learning segmentation to automate cell quantification in difficult samples, such as counting virally labeled neurons in tissue sections. 0:00 - Introduction and overview 10:08 - Introduction to JOBs and segment.ai 6:07 - Automated slide scanning 16:44 - Building a JOB 33:46 - Detecting tissue and counting cells using General Analysis 3 in JOBs 52:29 - Exporting results and measurement from General Analysis 105:42 - Training and using Segment.ai to detect neurons in tissue JOBS and general analysis scripts related to this workshop are available on Github here: https://github.com/lahammond/CI_ImageAnalysisProgram/tree/main/NIS_Elements Recorded on Thursday, December 9, 2021, as part of Cellular Imaging's 2021 Image Analysis Program by Luke Hammond (Director of Cellular Imaging, Zuckerman Institute, Columbia University) https://www.cellularimaging.org/