Description

Load image into MIA workspace. This module can be configured to import images from a variety of locations (selected using the "Import mode" control).

Parameters

Output image (default = "") Name assigned to the image.

Import mode (default = "Current file") Controls where the image will be loaded from:

Reader (default = "BioFormats") Set the reader for importing the image:

Sequence root name (default = "") Template filename for loading multiple image sequence files (those with names in the format "image0001.tif", "image0002.tif", "image0003.tif",etc.). Template filenames are constructed in a generic manner, whereby metadata values stored in the workspace can be inserted into the name using the notation "M{name}". This allows names to be created dynamically for each analysis run. The location in the filenam of the variable image number is specified using the "Z{0000}" notation, where the number of "0" characters specifies the number of digits. It is also necessary to specify the filepath (input file filepath stored as metadata value "M{Filepath}".

For example, loading the sequence "image0001.tif", etc. from the same folder as the input file would require the format "M{Filepath}\\imageZ{0000}.tif". Note: Backslash characters specifying the folder path need to be double typed (standard Java formatting).

Name format (default = "Generic (from metadata)") Method to use for generation of the input filename:

Comment (default = "") Root name for generation of Incucyte Zoom filenames. This will be added before the standard well and field values.

Extension (default = "") Extension for the generated filename.

Generic format (default = "") Format for a generic filename. Plain text can be mixed with global variables or metadata values currently stored in the workspace. Global variables are specified using the "V{name}" notation, where "name" is the name of the variable to insert. Similarly, metadata values are specified with the "M{name}" notation.

Available metadata fields (default = "") List of the currently-available metadata values for this workspace. These can be used when compiling a generic filename.

Include series number (default = "true") Option to include the current series number when compiling filenames. This may be necessary when working with multi-series files, as there will be multiple analyses completed for the same root file.

File path (default = "") Path to file to be loaded.

Channels (default = "1-end") Range of channels to be loaded for the current file. These can be specified as a comma-separated list, using a range (e.g. "4-7" will load channels 4,5,6 and 7) or as a range loading every nth channel (e.g. "4-10-2" will load channels 4,6,8 and 10). The "end" keyword will be converted to the total number of available channels at runtime.

Slices (default = "1-end") Range of slices to be loaded for the current file. These can be specified as a comma-separated list, using a range (e.g. "4-7" will load slices 4,5,6 and 7) or as a range loading every nth slice (e.g. "4-10-2" will load slices 4,6,8 and 10). The "end" keyword will be converted to the total number of available slices at runtime.

Frames (default = "1-end") Range of frames to be loaded for the current file. These can be specified as a comma-separated list, using a range (e.g. "4-7" will load frames 4,5,6 and 7) or as a range loading every nth frame (e.g. "4-10-2" will load frames 4,6,8 and 10). The "end" keyword will be converted to the total number of available frames at runtime.

Channel (default = "1") Channel to load when constructing a "Yokogawa" format name.

Load 3D stacks as (default = "Z-Stack") ImageJ will load 3D tifs as Z-stacks by default. This control provides a choice between loading as a Z-stack or timeseries.
Crop mode (default = "None") Choice of loading the entire image, or cropping in XY:

Reference image (default = "") The image to be displayed for selection of the cropping region if the cropping mode is set to "From reference".

Left coordinate (default = "0") Left coordinate limit for image cropping (specified in pixel units).

Top coordinate (default = "0") Top coordinate limit for image cropping (specified in pixel units).

Width (default = "512") Width of the final cropped region (specified in pixel units).

Height (default = "512") Height of the final cropped region (specified in pixel units).

Scale mode (default = "No scaling") Controls if the input image is scaled upon importing. This only works for scaling in X and Y (magnitudes determined by the "X scale factor" and "Y scale factor" parameters):

X scale factor (default = "1.0") Scale factor applied to X-axis of input images (if "Scale mode" is in an image scaling mode). Values <1 will reduce image width, while values >1 will increase it.

Y scale factor (default = "1.0") Scale factor applied to Y-axis of input images (if "Scale mode" is in an image scaling mode). Values <1 will reduce image height, while values >1 will increase it.

Set manual spatial calibration (default = "false") Option to use the automatically-applied spatial calibration or manually specify these values.

XY calibration (dist/px) (default = "1.0") Distance per pixel in the XY plane. Units for this are specified in the main "Input control" module.

Z calibration (dist/px) (default = "1.0") Distance per slice (Z-axis). Units for this are specified in the main "Input control" module.

Force bit depth (default = "false") Enable to force the output image to adopt a specific bit-depth.

Output bit depth (default = "8") Output bit depth of the loaded image.
Minimum input intensity (default = "0.0") Minimum intensity in the input image when in the native bit depth. This is used for scaling intensities to the desired bit depth.

Maximum input intensity (default = "1.0") Maximum intensity in the input image when in the native bit depth. This is used for scaling intensities to the desired bit depth.