Up: Component summary
Up: Component summary
Component
ConvertImage
Reads various image formats with LOCI Bioformats library (http://www.loci.wisc.edu/software/bio-formats). Saves each given channel number as a grayscale 16-bit PNG image. .TIF, .PNG, .ZVI, .LSM and .LIF are tested and supported.
| Source | Output |
|---|---|
 |  |
| Version | 1.2 |
|---|---|
| Bundle | anima |
| Categories | Image Transformation |
| Authors | Ville Rantanen (ville.rantanen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Matlab |
| Source files | component.xml bioformatread.m exoticread.m getexoticimages.m getexoticseries.m execute.m |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | BinaryFolder | Optional | A directory with image files. |
| inArray | Array<BinaryFolder> | Optional | An array of image files. |
Outputs| Name | Type | Description |
|---|---|---|
| outArray | Array<ImageList> | An array of Grayscale PNG images |
| out | ImageList | Grayscale PNG images. |
| list | CSV | List of images exported. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| allChannels | boolean | false | Extract all channels and series from all images. Shortcut for defining ch=-1,series=-1 |
| ch | float | 1 | Channel number to read. For RGB images R=1, G=2, B=3. For microscope manufacturer specific formats the number refers to acquisition order. -1 will extract all channels for single series. |
| depth | float | 0 | Bit depth of the image, if not autodetected (value=0) |
| group | string | "" | Grouping metadata for the extracted channel. |
| metadata | boolean | false | Extract all metadata. |
| nameString | string | "@ONAME@.@OEXT@_S@S@_C@C@.png" | Format of the written file name. Possible keywords: @ONAME@,@OEXT@,@S@,@C@,@GROUP@,@N@ (running index). |
| series | float | 1 | Image series, if choosing stack levels from multi-page image or animations. -1 for all series from single channel. |
Test cases| Test case | Parameters▼ | IN in |
IN inArray |
OUT outArray |
OUT out |
OUT list |
|---|---|---|---|---|---|---|
| case1 | properties | in | (missing) | (missing) | out | (missing) |
|
ch=2 |
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| case2 | properties | in | (missing) | (missing) | out | list |
|
ch=2, |
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| case3_array | properties | (missing) | inArray | (missing) | out | (missing) |
|
ch=2 |
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