Image Analysis and Data Management

Image Analysis

Bio-Imaging Resource Center provides a variety of image analysis resources/training:

• One-on-one user imaging data discussion, where we suggest the best software/method/pipeline for image analysis
• Writing of custom image analysis scripts, pipelines, batch processing
• Regular image analysis seminars and workshops
• Image Analysis User Group meetings
• One-on-one user training
• Helpdesk session, every Wednesday, 3-5pm

In addition, we encourage our users to contact us at the experimental design stage to have a discussion with our team of microscopy and image analysis experts, to ensure that the imaging data acquired will be appropriate for the planned analysis and research questions

Software

We have expertise in a variety of image analysis software/tools, which we use to help analyze our users’ imaging data

Open-source software: ImageJ/Fiji, QuPath, Napari, CellProfiler, Icy

Commercial Software: Imaris, Arivis, Aivia, Huygens, MetaMorph

Machine/Deep Learning frameworks: Weka, ilastik, Labkit StarDist, Cellpose, DeepImageJ, ZeroCostDL4Mic

For more information, please visit our Bio-Image Analysis GitHub page.

Here are the details on the available workstations and software for image processing and analysis.

Data Management

User data is transferred from the microscope acquisition computer to the BIRC server, which is for temporary storage and transfer, not for user data storage purpose. Users are advised to back up their data to their own computers/external hard drives ASAP.

Here is a list of the file formats for images acquired on different BIRC microscopes and the relevant data handling procedures: