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## Data structure requirements
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### **Images**
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Each image file must contain an image of at most 3 dimensions with the third dimension representing either depth (z coordinate) or time. Images are expected to be organised under one common root directory. For example, if the images are organized like this:
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▽ screen_images
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▽ plate1_replicate1
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▽ well001
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W001-P001-Z000-T0000-s1234-Cy3.tif
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W001-P001-Z000-T0000-s1234-EGFP.tif
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▷ well002
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▷ plate1_replicate2
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then the image root directory is screen_images. The organization of images under the root directory can follow any arbitrary structure as long as the
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The IDE can in principle read all image formats supported by BioFormats but has so far mostly been tested with TIFF.
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The image root directory must be accessible from the computer running the app.
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The primary requirement is a table of data points derived from images and a directory of corresponding images.
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### **Data points**
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##### Format
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... | ... | @@ -34,6 +18,28 @@ Note that the tables must have the same format, i.e. use the same delimiter and |
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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** and each cell of this column must reference only one file. Using the example above, 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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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. **All wells must be represented in the data file. Missing wells may cause unexpected behaviour.**
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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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| ---------- | ----------- | ----------- | ----------- | ----------- | ----------- | --------------- |----- | ------------ | ------ | ---- |
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| 1| 220 | 60 | 1 | 10 | experiment\_2021-08-03/replicate\_01/cells-P01-A07.tiff | 158 | 922 | 0.53238 | Plate01 | A07 |
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| 2| 356 | 71 | 1 | 10 | experiment\_2021-08-03/replicate\_01/cells-P01-A07.tiff | 127 | 1334 | 0.32007 | Plate01 | A07 |
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| 3| 108 | 119 | 1 | 10 | experiment\_2021-08-03/replicate\_01/cells-P01-A08.tiff | 93 | 549 | 0.70456 | Plate01 | A08 |
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### **Images**
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|
|
|
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Each image file must contain an image of at most 3 dimensions with the third dimension representing either depth (z coordinate) or time. Images are expected to be organised under one common root directory. For example, if the images are organized like this:
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▽ screen_images
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▽ plate1_replicate1
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▽ well001
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W001-P001-Z000-T0000-s1234-Cy3.tif
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W001-P001-Z000-T0000-s1234-EGFP.tif
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▷ well002
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▷ plate1_replicate2
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then the image root directory is screen_images. The organization of images under the root directory can follow any arbitrary structure as long as the data table associates each image file with the correct path (see Data points - Content above).
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The IDE can in principle read all image formats supported by BioFormats but has so far mostly been tested with TIFF.
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The image root directory must be accessible from the computer running the app.
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