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icbm-iupui / volumetric-tissue-exploration-analysis

3D TISSUE CYTOMETRY PLUGIN FOR IMAGEJ DOWNLOAD and INSTALL:
http://imagej.net/VTEA
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user manual #60

Closed matfallet closed 2 years ago

matfallet commented 4 years ago

Dear Seth,

Thanks for implementation of ROI import. Could you describe me how to import the ROI (COI) on my image. The second point is that I have no idea when I do the a scatterplot to see the Q1 and Q4 dots on my image ? It would be great to have a documentation and a video to explain to use your plugin. Thanks,

Mathieu

matfallet commented 4 years ago

Ok I can load a gate on my image by clicking on that gate but how to visualize two gates ?

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winfrees commented 4 years ago

Mathieu,

It looks like you are using v0.7. The features you requested (imageJ ROIs) and others(multiple highlights) are in the alpha version on the branch, ReEngineerLUTImplementation.

1) If you are comfortable building the plugin jar from a maven build in NetBeans or Eclipse, that might be easiest route for getting up and running both in terms of compiling as well as collecting all the dependencies.

2) I'll put together an alpha release that will incorporate the ROI import in the next couple days if that doesn't work.

3) Documentation... That is a part of the manuscript, it is coming.

4) I'm almost through drafting the manuscript, at which point there will be a BioArchives version and beta version referenced above will be become available through the ImageJ updater

Thanks for your interest, and nice work with your implementation, looks great!

Seth

winfrees commented 4 years ago

Im going to reopen this issue as it is critical for on-going use. It may be expanded and bifurcated to meet documentation needs.

winfrees commented 4 years ago

@matfallet, The prerelease with IMAGEJ1.0 ROIs is available (611c548). There may be dependencies that are needed, let me know if you have any trouble.

https://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/releases

matfallet commented 4 years ago

ok great, do you have a bug with czi image (300Mo, 6 channels)? The 1.0 version do not load my image (message : image loading ...). Thanks

matfallet commented 4 years ago

it doesn't work (load image) also with a tif image (4Mo) ) in 2D with 4 channels with the release v1.0 alpha r5. I just put plugin in the plugin folder. Best

winfrees commented 4 years ago

This is probably a missing dependency during VTEA plugin loading. I've added the necessary dependencies in a .zip file with the release. I'd also reinstall the plugin as I removed a dependency for a rather large .jar file. Attached image shows VTEA running with my test volume.

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winfrees commented 2 years ago

The website to begin to address this issue is being constructed at: vtea.wiki. This site will cover, installation, sketches demonstrating use with access to demonstration data, and FAQs and references. The website is a work-in-progress.

winfrees commented 2 years ago

Closing this issue as the website is ongoing. Specific requests for topics to cover on the website can be reopened as an issue here or at VTEA-site.