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I tried using starfish on a MERFISH image with Z = 4, C = 2 (4 depth planes and 2 fluorophore channels).
First I used the function write_experiment_json(), to seperate the image to 8 different image…
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Feedback:
I remember you saying that we would not need to download an image server, but rather use a Static one. I tried following these instructions: http://ronallo.com/iiif-workshop/image/image-ser…
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#### Description
If `local_max_peak_finder` is called with a cropped dataset, the x/y/z pixel coordinates in the `PerImageSliceSpotResults` table are the pixel offsets and not the pixel coordinates.
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ttung updated
4 years ago
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An user should leverage parallelism on HPC clusters to run starfish and process volumetric data like seqFISH data (s3://spacetx.starfish.data.public/seqfish/).
I am wondering if it is possible roughl…
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We need zarr support in R to be able to write expression matrices, and potentially to write hdf5 or other objects directly to zarr representations (like AnnData.write_zarr) See https://github.com/gdkr…
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After resaving the file we tried to run StarFish on it but it keeps failing even when playing with the version numbers ... see the image.sc post here:
https://forum.image.sc/t/unrecognized-version-…
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> As an exFISH Developer, I want starfish to provide an example of the processing of a single field of view of exFISH data so that I can establish it matches analysis done with my own tools.
We ha…
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Seems like `F.interpolation` is the problem. Is there any workaround for this ?
I follow the instruction on this [tutorial](https://awsdocs-neuron.readthedocs-hosted.com/en/latest/general/setup/neu…
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@christoffermattssonlangseth @xyanqian noted that starfish restricts global coordinate space to micrometers, but that it could be helpful to operate on the global space in pixels, as well.
Would o…
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ieahleen: "I have been transformed in a Ghost but I have Sand to buy in my reward column instead of the Opaque Potion..."
ieahleen: "update: Now that I am a snowman, I have the Opaque potion in the r…