Leginon

h1. Mosaic Click Target Finder

Mosaic Click Target Finder is a type of TargetFinder Node. It handles the loading, save,

displaying and target selection of a list of images and and their composit.

<highlights>

Required bindings for Mosaic Click Target Finder Node

<simplelist type="vert">

<member> Grid Targeting - (ImageTargetListPublishEvent) -> AcquisitionNodeAlias</member>

<member> AcquisitionNodeAlias- (AcquisitionImagePublishEvent) ->

MosaicClickTargetFinder</member>

<member> MosaicClickTargetFinder - (ImageTargetListPublishEvent) -> AcquisitionNodeAlias </member>

<member>ClickTargetFinder - (ReferenceTargetListPublishEvent) -> AlignZeroLossPeak or

MeasureDose</member>

</simplelist>

</highlights>

<highlights>

Required bindings for MosaicClickTargetFinder Node if Reference Targets are used

<simplelist type="vert">

<member>MosaicClickTargetFinder - (ReferenceTargetListPublishEvent) -> AlignZeroLossPeak

or MeasureDose</member>

</simplelist>

</highlights>

h2.  Toolbar

*  Tiles = Choose The Mosaic Tiles label (aka atlas label) to display. Mosaic Tiles

are a list of images collected by an Acquisition node upstream.

*  Mosaic = Select how large the mosaic atlas image will be and what calibration is

used to create it.

*  Refresh = Refresh the "Mosaic" selector to the current choices in the

database.

*  Show Position = When clicked, the current microscope position (orange crosshair)

will be updated on the atlas image.

*  Find Squares = An automatic algorithm for detecting squares on the atlas

image.

*  Submit Targets = Submit the selected squares for processing.

h2.  Tiles

*  Load tiles from mosaic = Choose The Mosaic Tiles label (aka atlas label) to

display. Mosaic Tiles are a list of images collected by an Acquisition node

upstream.

* Reset = Clears the loaded list in the Mosaic Click Target Finder, and therefore

clears the mosaic image shown.

h2.  Mosaic Settings

*  Calibration parameter (stage position | image shift | modeled stage position) =

Select the type of calibration used to create the atlas. Stage Position should be used.

This determines how the node creates the pixel shifts for each tile image in order to

"paste" it to the right position of the mosaic image. Each acquired image in the

database has the full information on its stage position and image shift. This pull-down

selector determines which items the subnode look into for the conversion into pixel

shift.

*  Scale image to "1000" pixels in largest dimension = When enabled, the mosaic atlas

will be scaled to this image size.

*  Mosaic Image (Create | Save) = Create and save the large mosaic atlas to the

database.

h2.  Image Control Panel

*  acquisition = Use this to select NEW targets shown in a greeen crosshair.

*  done = The done targets (squares already visited) will be shown with a red

crosshair.

*  position = The current position of the microscope relative to the grid is shown

with an orange crosshair.

*  image = The atlas image is shown.

*  Filtered = This is used for the automatic square selection algorithm

*  Thresholded = This is also used the the automatic square selection algorithm

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[[Matrix Calibrator|< Matrix Calibrator]] | [[Mosaic Target Maker|Mosaic Target Maker >]]

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