Commit 918d1e1e authored by Jean-Karim Heriche's avatar Jean-Karim Heriche

Updated data format description in README.

parent c885aa88
......@@ -16,8 +16,11 @@ Each image file must contain an image of at most 3 dimensions with the third dim
then the image root directory is screen\_images.
The IDE can in principle read all image formats supported by BioFormats but has so far only been tested with TIFF, PNG and JPEG.
#### Data points
Image-derived data are expected to be in table format with data points in rows and stored in a tab- or comma-separated plain text file. The table must have column headers with unique column names. 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.
The IDE references ROIs by the coordinates of 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).
##### Format
Image-derived data are expected to be in table format with data points in rows and stored in a tab- or comma-separated text file using ASCII or UTF-8 encoding. The table must have column headers with unique column names and all columns must have a header. For numbers, the decimal separator must be . (dot) and no separator for thousands is allowed.
##### Content
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.
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).
### Using the IDE
#### Requirements
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