Image Reader

Reads images from various file formats supported by the Bio-Formats library and imports them to the KNIME-internal image format. A list of the supported formats can be found here: http://loci.wisc.edu/bio-formats/formats . Image can also be downloaded and read from URLs (e.g. http://...). The URLs have to be provided via the input table (as strings).

Options

File browser

Choose your image files here and add them to the list of selected files. An image preview is available which will also help you to determine, whether an image format is supported or not. The list of the core meta data gives you some more information about the image object.

Additional Options

OME-XML-metadata

You can either add a column containing the metadata formated as an OML-XML-String, read only the metadata from the images files, or just read the images (default). (for more details see: http://www.ome-xml.org/ ).

Read non OME-XML Metadata

Read metadata that is not part of the ome-xml specification. It will be appended as XML annotation to the ome-xml metadata.

Image Factory

Defines the way how the images are created and therewith kept in memory: Array Image Factory (stored as ONE array; pros: fast pixel access; cons: limited number of pixels per image), Planar Image Factory (each plane is stored in an array; pros: images are read faster; cons: limited number of pixels in an XY-plane, slower pixel access), and Cell Image Factory (multiple arrays of fixed sizes are used, pros: unlimited number of pixels per images; cons: very slow pixel reading and pixel access))

Pixel type

Set the numeric type of the pixel values, this can save memory when reading e.g. a binary image saved as integer image.
Attention this option can lead to unexpected results if the selected pixel type does not fit the read data. Make sure you are not reading unsigned values into a signed data type or signed values into an unsigned data type. In most cases the right choice is "Automatic".

Check file format for each file

Checks for each file individually the file-format, if checked. Else, the file format as assumed to be the same for all files and only if the reading fails, the new file format will be determined.

File name column in optional table

If another node with a string column is plugged to the optional in-port, the column, which contains the potential file paths, can be selected.

Read all series

Some image file formats might contain multiple images (called series). One can either read all available series (each appended as own table row) or one can specify with a range which indices from the series should be read.

Load group files

If selected, related group files will be read as well.

Subset Selection

Image Subset Selection

Select the image planes here you actually want to open. Use shift or ctrl-keys to mark more than one plane or the "all"-checkbox to select all available planes. Detailed informations about the sizes of the individual dimensions can be obtained from the image metadata.

Alternatively, selecting subsets can be done in three ways using the text field below each selection list:

Discrete Element Selection Every element that shall be selected can be entered on it's own, separated by commas. e.g. "1, 5, 8, 9"

Cohesive Element Selection Selecting a complete region "from" a given value "to" another can be done by putting a hyphen between two values, marking the first as the region start and the second as the end. Comma-separation still holds and can separate either complete regions, or regions and discrete selections. e.g. 1-5, 8-10, 11

Function Based Selection Selection values based on a given function can be done by marking the function with a leading "f=" and entering the desired functionality thereafter. Any single variable function or constant contained within the javascript math package can be used with standard javascript syntax. (e.g. math.pow(2, i) for selecting 2, 4, 8,...)

Combining The above mentioned functionalities can be arbitrarily intermingled as every comma separated entry is read and interpreted on it's own. e.g. Selecting all Values from 1-10, every eleventh entry and the twentieth entry for some reason can be done by entering: "1-10, 20, f=11*i"

Views

Image Viewer

Displays the selected cells with their associated viewer if it exists.

Workflows

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Developers