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Note that the tables must have the same format, i.e. use the same delimiter and have the same columns in the same order. This also assumes that the tables are the only .csv files in the directory.
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##### Content
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To link data points to images, the table should include one column with the **path to image files relative to the image root directory** (see [images file system organisation](#file-system-organisation)) and each cell of this column must reference only one file. Using the [image directory example below](#images), the image root directory is 'screen\_images' and therefore the table column for data points associated with image W001-P001-Z000-T0000-s1234-Cy3.tif should contain the relative path 'plate1_replicate1/well001/W001-P001-Z000-T0000-s1234-Cy3.tif'. There can be multiple columns with links to images but only two can be used simultaneously in the IDE.
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The IDE references ROIs by the **coordinates of an anchor point** (e.g. the ROI centre) therefore there should be a column for each of the relevant coordinates: x, y and either z or t. Coordinates (x,y) must be in pixels relative to the top left corner of the image (which is pretty much the standard for image analysis software).
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The IDE references ROIs by the **coordinates of an anchor point** (e.g. the ROI centre) therefore there should be a column for each of the relevant coordinates: x, y and either z or t or channel. Coordinates (x,y) must be in pixels relative to the top left corner of the image (which is pretty much the standard for image analysis software).
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For high-throughput microscopy data, the table should have separate columns for plate and well identifiers. Wells must be identified either by indices starting from 1 in the top left corner of the plate and incremented by row from left to right or by row/column coordinates with rows identified by letters and columns by numbers with well A1 in the top left corner of the plate. When using versions < 1.1.0, all wells must be represented in the data file as missing wells may cause unexpected behaviour in these early versions. In newer versions, plate size must be specified if wells are missing from the data.
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##### Data table example
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| Object\_ID | Centroid\_X | Centroid\_Y | Centroid\_Z | Time\_frame | Image\_Path | Mean\_intensity | Area | Eccentricity | Plate | Well |
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### **Images**
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##### Format
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The IDE can read all image formats supported by BioFormats but has so far mostly been tested with TIFF. However, its image viewer can currently display images of at most 3 dimensions with the third dimension representing either depth (z coordinate) or time. To deal with images of higher dimensions, the IDE merges channels into a colour image.
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The IDE can read all image formats supported by BioFormats but has so far mostly been tested with TIFF. However, its image viewer can currently display images of at most 3 dimensions with the third dimension representing either depth (z coordinate), time or channel. To deal with images of higher dimensions, the IDE merges channels into a colour image.
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##### File system organisation
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When the IDE runs on a user’s computer (or a server), the images can be on any file system the user has access to from that computer. Images are expected to be organised under one common root directory. This directory is a top-level directory under which all images can be found. For example, if the images are organized like this:
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