linux target platform

[hkvaka]

Hi

I am looking at integrating the nuget package in to my solution .NET 6 running on a Linux target platform

I am getting the following error while installing the package, will this package work for Linux platform

[BiologyTools]

I have just uploaded a revised version of the package updated with the latest Bioformats version as well as IKVM. When installing add the BioFormats.NET6 package and add IKVM 8.4.5. https://www.nuget.org/packages/BioFormats.NET6/6.12.0 Thank you for noticing this issue.

[hkvaka]

Thank you for quickly resolving this issue, I can now install both the packages as suggested.
could you please point me to any documentation/ code snippet how I can use the library, basically I wanted to generate deep zoom images for z stack whole slide images for .ndpi/svs/mrxs files

[BiologyTools]

The whole slide images I have used with BioGTK are opened by the BioImage.OpenOMETiled function. 'OpenOMETiled (string file, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY)' https://biologytools.github.io/class_bio_g_t_k_1_1_bio_image.html However the images I have do not have Z-depth only multiple pyramidal resolutions. If the images open up correctly in BioGTK you should be able to use the open tile function I mentioned. Let me know what format your images are in?

[hkvaka]

Many Thanks for a quick reply

The image formats I am looking to process are ndpi, svs and mrxs. to start with I am looking to process a large ndpi file

[BiologyTools]

The files I have tested with were czi. But if they open up correctly with BioGTKApp. You should be able to use the "Crop" filter to get stacks from the whole slide image. You can use the Recorder to get code that should work in a script.

[hkvaka]

I've tried to create a new BioImage by passing the file path and getting no Information from the image object, is this the expected way to load an image, could you suggest how to load an image and get metadata

[BiologyTools]

The documentation needs to be updated I will be doing so today. Here is how to use the library to open part of an image.
App.Initialize();
//BioImage.OpenOME(string file, int series, bool openInNewTab, bool addToImages, bool tile, int tilex, int tiley, int tileSizeX, int tileSizeY)
//Note the series parameter is the pyramidal resolution for pyramidal images.
BioImage bi = BioImage.OpenOME("file", 0, false, true, 0,0,800,800);
BioImage.SaveOME("file to save to",bi.ID);

[hkvaka]

Thank you for the code snippet when I try to run the App.Initalize() also tried BioImage..Initalize() getting the below error

[BiologyTools]

It's throwing an error when trying to initialize the OME library using IKVM. Add a reference to the bioformats-package.dll which should be included in your project when you installed Bioformats.NET6.

[BiologyTools]

I noticed you are using Visual Studio Code for development I use Visual Studio 2022 Community for Windows. I'm not sure if you can get it to compile with Visual Studio Code.

[hkvaka]

I am using VS 2022 as well and noticed the bioformats-package.dll included in the proj files and marked it as always copy
I can see the dll being copied to the output directory but still get the above error

[BiologyTools]

Is it showing up correctly in the Dependencies?

[hkvaka]

My dependencies look like this

[BiologyTools]

Right click on dependencies and click "Add Project Reference..." then browse to the directory of your project and select the "bioformats_package.dll". Then you should have a assemblies reference like mine.

[hkvaka]

Thank you I've referenced it from the bin directory where its copied physically, not sure if thats what was suggested and now get a different error