Modules

Load image

Load image into MIA workspace.

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

Parameter Description
Output image Name assigned to the image.
Import mode 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 (alphabetical)" will load a series of images matching a specified name format in alphabetical order. The format of the names to be loaded is specified by the "Sequence root name" parameter.
  • "Image sequence (zero-based)" will load a series of images with numbered elements. The format of the names to be loaded is specified by the "Sequence root name" parameter.
  • "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 Set the reader for importing the image:
  • "Bio-Formats" will use the Bio-Formats plugin. This is best for most cases (especially proprietary formats).
  • "ImageJ" will use the stock ImageJ file reader.
Sequence root name 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 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 Root name for generation of Incucyte Zoom filenames. This will be added before the standard well and field values.
Extension Extension for the generated filename.
Generic format 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.
Include series number 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 Path to file to be loaded.
Series mode Controls which series should be loaded for multiseries files (e.g. Leica LIF files):
  • "Current series" will load the same series as the current root file (i.e. that selected via "Input control").
  • "Specific series" will load a specific series specified by the "Series number"parameter.
Series number If a specific series is being loaded ("Series mode" set to "Specific series"), this is the series that will be used.
Channels 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 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 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 Channel to load when constructing a "Yokogawa" format name.
Crop mode 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.
  • "Object collection limits" will crop to the limits of the objects in the collection specified by "Objects for limits".
Reference image The image to be displayed for selection of the cropping region if the cropping mode is set to "From reference".
Left coordinate Left coordinate limit for image cropping (specified in pixel units).
Top coordinate Top coordinate limit for image cropping (specified in pixel units).
Width Width of the final cropped region (specified in pixel units).
Height Height of the final cropped region (specified in pixel units).
Objects for limits If "Crop mode" is set to "Object collection limits", this is the object collection that will define the limits of the cropped region.
Scale mode 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 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 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.
Dimension mismatch mode If loading an image sequence from separate files, this parameter controls how dimensions mismatches between images are handled:
  • "Crop (centred)" The images will be centred-aligned and cropped to the smallest image dimensions. This prevents empty borders around some images, but means information is lost from larger images.
  • "Pad (centred)" The images will be centre-aligned and padded to the largest image dimensions. This prevents any image infomation being lost at edges, but means smaller images will have borders.
  • "Disallow (fail upon mismatch)" All images must have exactly the same dimensions. If a dimension mismatch is detected, the image loading process will fail.
Pad intensity mode If loading an image series from separate files and "Dimension mismatch mode" is set to "Pad (centred)" this parameter will control the intensity of the padding border around images smaller than the largest loaded image.
Set manual spatial calibration Option to use the automatically-applied spatial calibration or manually specify these values.
XY calibration (dist/px) Distance per pixel in the XY plane. Units for this are specified in the main "Input control" module.
Z calibration (dist/px) Distance per slice (Z-axis). Units for this are specified in the main "Input control" module.
Set manual temporal calibration Option to use the automatically-applied temporal calibration or manually specify this value.
Frame interval (time/frame) Time duration between the start of consecutive frames. Units for this are specified in the main "Input control" module.
Force bit depth Enable to force the output image to adopt a specific bit-depth.
Output bit depth Output bit depth of the loaded image.
Minimum input intensity 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 Maximum intensity in the input image when in the native bit depth. This is used for scaling intensities to the desired bit depth.