qupath/qupath-extension-align

QuPath extension to interactively align images

QuPath

QuPath is open source software for bioimage analysis.

Features include:

• Lots of tools to annotate and view images, including whole slide & microscopy images
• Workflows for brightfield & fluorescence image analysis
• New algorithms for common tasks, including cell segmentation, tissue microarray dearraying
• Interactive machine learning for object & pixel classification
• Customization, batch-processing & data interrogation by scripting
• Easy integration with other tools, including ImageJ

To download QuPath, go to the Latest Releases page.

For documentation, see https://qupath.readthedocs.io

For help & support, try image.sc or the links here

To build QuPath from source see here.

If you find QuPath useful in work that you publish, please cite the publication!

QuPath is an academic project intended for research use only. The software has been made freely available under the terms of the GPLv3 in the hope it is useful for this purpose, and to make analysis methods open and transparent.

Development & support

QuPath is being actively developed at the University of Edinburgh by:

• Pete Bankhead (creator)
• Fiona Inglis
• Alan O'Callaghan
• Léo Leplat
• Laura Nicolás-Sáenz

Past QuPath dev team members:

• Melvin Gelbard
• Mahdi Lamb

For all contributors, see here.

This work is made possible in part thanks to funding from:

• Wellcome Trust Technology Development Grant (2022-Present)
• CZI Essential Open Source Software for Science, Cycle 4 (2022-Present)
• CZI Essential Open Source Software for Science, Cycle 1 (2020-2022)
• Wellcome Trust / University of Edinburgh Institutional Strategic Support Fund (ISSF3) (2019-2020)

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Background

QuPath was first designed, implemented and documented by Pete Bankhead while at Queen's University Belfast, with additional code and testing by Jose Fernandez.

Versions up to v0.1.2 are copyright 2014-2016 The Queen's University of Belfast, Northern Ireland. These were written as part of projects that received funding from:

• Invest Northern Ireland (RDO0712612)
• Cancer Research UK Accelerator (C11512/A20256)

qupath-extension-align's Issues

Error message when installing qupath-extension-align-0.4.0.jar

I am a new QuPATH user, using version 0.4.3. I am looking to align serial sections for multiplex immunofluorescence stains.

I downloaded the "qupath-extension-align-0.4.0.jar" file from this page. I followed the instructions on the following webpage to install the extension: https://qupath.readthedocs.io/en/0.4/docs/intro/extensions.html

I dragged the .jar file into the main QuPATH window and selected a user directory to store the extension in. However, it did not properly import. I closed QuPATH and reopened as recommended. The following error message came up (see attached photo). It seems that it is incompatible with my QuPATH version. I know the .jar file says 0.4.0 and my version is 0.4.3, but I assumed this extension would be compatible with all 0.4.x versions. Maybe this is the issue though?

I am very new to both QuPATH and coding in general, so am not sure where to start with troubleshooting.

Thanks!