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Load image
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
- Description: Name assigned to the image.
- Type: OutputImageP
- Import mode
- Description: File reader mode to use.
- "Current file" (default option) will import the current root-file for the workspace.
- "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 a specific location. - Type: ChoiceP
- Default value: Current file
- Choices:
- All in current folder
- Current file
- From ImageJ
- Image sequence
- Matching format
- Specific file
- Reader
- Description: 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. - Type: ChoiceP
- Default value: BioFormats
- Choices:
- Sequence root name
- Name format
- Description: 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.
- Type: ChoiceP
- Default value: Generic (from metadata)
- Choices:
- Generic (from metadata)
- Huygens
- Incucyte short filename
- Yokogowa
- Comment
- Description: Root name for generation of Incucyte Zoom filenames. This will be added before the standard well and field values.
- Type: StringP
- Extension
- Description: Extension for the generated filename.
- Type: StringP
- Generic format
- Description: 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.
- Type: StringP
- Available metadata fields
- Description: List of the currently-available metadata values for this workspace. These can be used when compiling a generic filename.
- Type: TextAreaP
- Include series number
- Description: 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.
- Type: BooleanP
- Default value: true
- File path
- Description: Path to file to be loaded.
- Type: FilePathP
- Channels
- Description: 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.
- Type: StringP
- Default value: 1-end
- Slices
- Description: 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.
- Type: StringP
- Default value: 1-end
- Frames
- Description: 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.
- Type: StringP
- Default value: 1-end
- Channel
- Description: Channel to load when constructing a "Yokogawa" format name.
- Type: IntegerP
- Default value: 1
- Load 3D stacks as
- Description: ImageJ will load 3D tifs as Z-stacks by default. This control provides a choice between loading as a Z-stack or timeseries.
- Type: ChoiceP
- Default value: Z-Stack
- Choices:
- Crop mode
- Description: 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. - Type: ChoiceP
- Default value: None
- Choices:
- Reference image
- Description: The image to be displayed for selection of the cropping region if the cropping mode is set to "From reference".
- Type: InputImageP
- Left coordinate
- Description: Left coordinate limit for image cropping (specified in pixel units).
- Type: IntegerP
- Default value: 0
- Top coordinate
- Description: Top coordinate limit for image cropping (specified in pixel units).
- Type: IntegerP
- Default value: 0
- Width
- Description: Width of the final cropped region (specified in pixel units).
- Type: IntegerP
- Default value: 512
- Height
- Description: Height of the final cropped region (specified in pixel units).
- Type: IntegerP
- Default value: 512
- Scale mode
- Type: ChoiceP
- Default value: No scaling
- Choices:
- No scaling
- Scaling (no interpolation)
- Scaling (bilinear)
- Scaling (bicubic)
- X scale factor
- Type: DoubleP
- Default value: 1.0
- Y scale factor
- Type: DoubleP
- Default value: 1.0
- Set manual spatial calibration
- Description: Option to use the automatically-applied spatial calibration or manually specify these values.
- Type: BooleanP
- Default value: false
- XY calibration (dist/px)
- Description: Distance per pixel in the XY plane. Units for this are specified in the main "Input control" module.
- Type: DoubleP
- Default value: 1.0
- Z calibration (dist/px)
- Description: Distance per slice (Z-axis). Units for this are specified in the main "Input control" module.
- Type: DoubleP
- Default value: 1.0
- Force bit depth
- Description: Enable to force the output image to adopt a specific bit-depth.
- Type: BooleanP
- Default value: false
- Output bit depth
- Description: Output bit depth of the loaded image.
- Type: ChoiceP
- Default value: 8
- Choices:
- Minimum input intensity
- Description: Minimum intensity in the input image when in the native bit depth. This is used for scaling intensities to the desired bit depth.
- Type: DoubleP
- Default value: 0.0
- Maximum input intensity
- Description: Maximum intensity in the input image when in the native bit depth. This is used for scaling intensities to the desired bit depth.
- Type: DoubleP
- Default value: 1.0