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camicroscope / caMicroscope

Digital pathology image viewer with support for human/machine generated annotations and markups.
BSD 3-Clause "New" or "Revised" License
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Is it possible to use caMicroscope with an iipimage-server installed separately? #574

Closed catweis closed 1 year ago

catweis commented 1 year ago

Describe the solution you'd like I have an organized set of folders with WSI and adjacent other files. To view and annotate, I want to use caMicroscope. Is it possible to install (for example) on one Linux machine an iipimage-sever to present the images and view it with a caMicroscope installation on another machine? I want to avoid uploading or copying my image files.

birm commented 1 year ago

The field IIP_PATH for our backend controls how the proxy is set up for iip. (see https://github.com/camicroscope/Distro/blob/4f107ac106b8ebd0422de32b6e9d69d00d0f517d/caMicroscope.yml#L37). Also it's important to note that the IIP version we use is configured with openslide, and vanilla iip probably won't work on your slides.

I'd like to point out that this would mean that our ordinary slide metadata extraction "loading" process would not work, but this could be resolved by manually adding the metadata into the mongo database.

Please let me know if you want help with any of this; perhaps we could add some config/helpers for this kind of architecture.

catweis commented 1 year ago

Thank you very much for your fast response. Then I am trying to install your “iip-version” on one server and the rest (with modified docker compose) on the other machine. For me is crucial that there is no copying or loading of the WIS required. Would that also be not the case with an installation on one system? May I ask what the metadata does comprise?

On 17 Feb 2023, at 22:46, Ryan Birmingham @.***> wrote:

The field IIP_PATH for our backend controls how the proxy is set up for iip. (see https://github.com/camicroscope/Distro/blob/4f107ac106b8ebd0422de32b6e9d69d00d0f517d/caMicroscope.yml#L37). Also it's important to note that the IIP version we use is configured with openslide, and vanilla iip probably won't work on your slides.

I'd like to point out that this would mean that our ordinary slide metadata extraction "loading" process would not work, but this could be resolved by manually adding the metadata into the mongo database.

Please let me know if you want help with any of this; perhaps we could add some config/helpers for this kind of architecture.

— Reply to this email directly, view it on GitHub https://github.com/camicroscope/caMicroscope/issues/574#issuecomment-1435312743, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY4ZSRVLKE4GLVVJPMZEYTWX7WUFANCNFSM6AAAAAAU72UZQI. You are receiving this because you authored the thread.

birm commented 1 year ago

See https://github.com/camicroscope/Distro/blob/4f107ac106b8ebd0422de32b6e9d69d00d0f517d/config/test_seed.js#L3 for a reasonably minimal version of what's required. Mpp is "microns per pixel" and is needed for any tool which uses physical measurements.

tomararun commented 1 year ago

Is this still open? Can I contribute to it.

birm commented 1 year ago

Hi @catweis , I'm marking this as stale/resolved, but feel free to comment/reopen if this needs more discussion or help. Thank you!

tomararun commented 1 year ago

Thank you for notifying me. I acknowledge that issue #574 has been closed as completed.

On Fri, 11 Aug 2023 at 02:39, Ryan Birmingham @.***> wrote:

Closed #574 https://github.com/camicroscope/caMicroscope/issues/574 as completed.

— Reply to this email directly, view it on GitHub https://github.com/camicroscope/caMicroscope/issues/574#event-10064061944, or unsubscribe https://github.com/notifications/unsubscribe-auth/AW4IDKXHI4I43T4YFDT3L2TXUVE2JANCNFSM6AAAAAAU72UZQI . You are receiving this because you commented.Message ID: @.***>