Custom vendor format

Derek Magee D.R.Magee at
Mon May 12 22:42:28 EDT 2014

Hi Tim,

I had vaguely in mind something similar (although XML based). Does anyone know if such a general text+images format exists? I know hamamatsu (sp) is along these lines, but it seems to have restrictions on image size and no support for overlap. Tim (and others) - happy to collaborate on this. I'm working on a similar viz application that I plan to release for free soon(ish), so get in touch off list.


"Blattner, Timothy J." <timothy.blattner at> wrote:


I am working on a project at NIST (National Institute of Standards and Technology) that deals with image stitching. The images are acquired using a microscope stage that takes overlapping images. One of the results of the stitching yields an 80k x 80k pixels image. I am looking into visualization software for these very large images and stumbled across open slide.

I should not have a problem with outputting the final image into a format that is supported by OpenSlide, but the idea came to me that it might be exciting to provide a position list to OpenSlide instead.

So I was wondering if it would be possible for me to add support into OpenSlide to visualize images that are constructed using a CSV file that contain ‘path_to_file, x_pixel_position, y_pixel_position’. Now the tricky part with this technique is we would need to do blending on the overlapping regions, so either linear, average, or overlay; however, I think that it will not be expensive to do blending on the fly.

I have peaked around the source code and looked at various image format vendors, and wanted to get some input on where to start with this project and what would be the best way to hook it into OpenSlide.



Timothy Blattner

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