Parameters
Output image (default = "") Name assigned to the image.
Import mode (default = "Current file") Controls where the image will be loaded from:
- "Current file" (default option) will import the current root-file for the workspace (this is the file specified in the "Input control" module).
- "From ImageJ" will load the active image fromm ImageJ.
- "Image sequence" will use the root-file for the workspace as the basis for loading a series of images with numbered suffixes.
- "Matching format" will load the image matching a filename based on the root-file for the workspace and a series of rules.
- "Specific file" will load the image at the location specified by "File path".
Reader (default = "BioFormats") Set the reader for importing the image:
- "BioFormats" will use the BioFormats plugin. This is best for most cases (especially proprietary formats).
- "ImageJ" will use the stock ImageJ file reader.
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:
- "Generic (from metadata)" (default) will generate a name from metadata values stored in the current workspace.
- "Huygens" will generate a name matching the SVI Huygens format, where channel numbers are specified as "ch00", "ch01", etc.
- "Incucyte short filename" will generate a name matching the short Incucyte Zoom format. The root name is specified as the parameter "Comment".
- "Yokogowa" will generate a name matching the Yokogawa high content microscope name format.
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:
- "None" (default) will load the entire image in XY.
- "Fixed" will apply a pre-defined crop to the input image based on the parameters "Left", "Top","Width" and "Height".
- "From reference" will display a specified image and ask the user to select a region to crop the input image to.
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):
- "Scaling (bicubic)" Scales the input images using a bicubic filter. This leads to smooth intensity transitions between interpolated pixels.
- "Scaling (bilinear)" Scales the input images using a bilinear filter. This leads to smooth intensity transitions between interpolated pixels.
- "No scaling" (default) Input images are not scaled. They are loaded into the workspace at their native resolutions.
- "Scaling (no interpolation)" Scales the input images using a nearest-neighbour approach. This leads to a "blocky" apppearance to scaled images.
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.