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Merge pull request #501 from will-moore/settings_docs
Add docs/settings.md
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README.rst

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@@ -31,40 +31,8 @@ https://omero-guides.readthedocs.io/en/latest/iviewer/docs/index.html
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Settings
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========
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OMERO limits the size of Z-projections to reduce load on the server.
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The limit is defined as the number of bytes of raw pixel data in a Z-stack and
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the OMERO.server default is equivalent to 1024 * 1024 * 256 bytes.
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For example, a single-channel 8-bit image (1 byte per pixel) of XYZ size
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1024 * 1024 * 256 is equal to the default threshold.
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To double the limit, use::
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$ omero config set omero.pixeldata.max_projection_bytes 536870912
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If you wish to set a threshold for iviewer that is *lower* than for the server:
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$ omero config set omero.web.iviewer.max_projection_bytes 268435456
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NB: Z-projection is not supported for tiled images in OMERO
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(Images larger than 2048 * 2048 pixels per plane are tiled in iviewer).
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OMERO uses Spectrum Color Picker for selecting ROI colors.
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The roi_color_palette option allows you to specify a grid of colors for users to choose for ROIs.
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Define rows with brackets, and use commas to separate values. By default, only the first color of each row is shown.
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A full grid is shown when the default color picker is hidden (see below)
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To define a color palette use::
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$ omero config set omero.web.iviewer.roi_color_palette "[rgb(0,255,0)],[darkred,red,pink],[#0000FF]"
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To hide the default color picker (and show a grid for the color palette), set show_palette_only to true
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You must define a palette and each row can display 4 colors::
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$ omero config set omero.web.iviewer.show_palette_only true
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When working with other images (coregistering MRIs for example), it is necessary to be able to mirror an image.
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There is now experimental support for runtime image mirroring. To enable mirroring set enable_mirror to true.
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$ omero config set omero.web.iviewer.enable_mirror true
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See the `OMERO.iviewer settings <https://github.com/ome/omero-iviewer/blob/settings_docs/docs/settings.md>`_
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for details on how to configure various settings.
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Known issues
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============

docs/settings.md

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OMERO.iviewer settings
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======================
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Max projection bytes
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--------------------
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OMERO limits the size of Z-projections to reduce load on the server.
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The limit is defined as the number of bytes of raw pixel data in a Z-stack and
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the OMERO.server default is equivalent to 1024 * 1024 * 256 bytes.
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For example, a single-channel 8-bit image (1 byte per pixel) of XYZ size
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1024 * 1024 * 256 is equal to the default threshold.
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To double the limit, use::
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$ omero config set omero.pixeldata.max_projection_bytes 536870912
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If you wish to set a threshold for iviewer that is *lower* than for the server:
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$ omero config set omero.web.iviewer.max_projection_bytes 268435456
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NB: Z-projection is not supported for tiled images in OMERO
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(Images larger than 2048 * 2048 pixels per plane are tiled in iviewer).
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ROI color palette
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-----------------
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OMERO uses Spectrum Color Picker for selecting ROI colors.
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The `roi_color_palette` option allows you to specify a grid of colors for users to choose for ROIs.
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Define rows with brackets, and use commas to separate values. By default, only the first color of each row is shown.
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A full grid is shown when the default color picker is hidden (see below).
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To define a color palette use::
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$ omero config set omero.web.iviewer.roi_color_palette "[rgb(0,255,0)],[darkred,red,pink],[#0000FF]"
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To hide the default color picker (and show a grid for the color palette), set `show_palette_only` to true
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You must define a palette and each row can display 4 colors::
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$ omero config set omero.web.iviewer.show_palette_only true
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Enable mirror
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-------------
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When working with other images (coregistering MRIs for example), it is necessary to be able to mirror an image.
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There is now experimental support for runtime image mirroring. To enable mirroring set `enable_mirror` to true.
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$ omero config set omero.web.iviewer.enable_mirror true
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Max active channels
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-------------------
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By default, iviewer limits the maximum number of active channels to 10. Rendering high numbers of channels
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at once puts increased load on the server and it is rarely necessary to visualise more channels at once.
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$ omero config set omero.web.iviewer.max_active_channels 20
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NB: If the iviewer is using the [image region microservice](https://github.com/glencoesoftware/omero-ms-image-region)
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then it will query the `max-active-channels` supported by the microservice, which is also set to 10 by default. This will override any value in the iviewer settings.
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ROI page size
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-------------
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The pagination page size for the ROIs list is 500 by default. Loading larger numbers will take longer.
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The pagination is also constrained by the underlying `omero-web` JSON API, so you need to set both these
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settings if you want to increase the limit.
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$ omero config set omero.web.iviewer.roi_page_size 1000
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$ omero config set omero.web.api.max_limit 1000

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