Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
Has anybody requested support for ScanImage TIFF files in Bio-Formats yet? If not, LOCI may implement this.
where can I download the java package (what is it called)for the bioformats library so I can use the SVSReader in loci.formats.in inside of eclipse because the only package i've downloaded seems to be used for imageJ only(http://downloads.openmicroscopy.org/bio-formats/5.1.10/)
hi @wongmac — instructions for using Eclipse are available at https://www.openmicroscopy.org/site/support/bio-formats5.1/developers/building-bioformats.html?highlight=eclipse#eclipse though these assume you are building from source. If you are using maven in Eclipse, then you can list Bio-Formats as a dependency, though you’ll need to point to non-standard repository.
I second the suggestion to use Maven. You could look at https://github.com/fiji/fiji for an example of including Bio-Formats. You need the
formats-gpl component in particular.
How can I set the current file so I can uses the svs reader of the bioformats library? https://downloads.openmicroscopy.org/bio-formats/5.1.0/api/loci/formats/IFormatReader.html#getCurrentFile()
Here is where it reads bytes from one plane at a time in a loop.
And here is where it assigns the filename to the reader, using the
setId method. The file format is autodetected from the contents of the file.
If anything is not clear in there, let us know here, and we will explain. Good luck. :-)
Note that that example does a lot of extra stuff you probably don't need for your use case, like wrapping up the reader in some layers.
For you, it is likely enough to just do:
ImageReader r = new ImageReader();
r.setId("/path/to/my.svs");
for (int s=0; s<r.getSeriesCount(); r++) {
r.setSeries(s);
for (int i=0; i<r.getImageCount(); i++) {
byte[] plane = r.openBytes(i);
}
}
And if you need to extract metadata, there are various ways of doing that; see this page for a primer.
You need to ask the reader for the bits per pixel, type, etc., unfortunately. But it is doable.
does the make2DDataArray function given by the DataTools class allow me to retrieve the RGB values somehow? (what data type is stored inside of the array) and how can I retrieve the rgb or hsi values from the byte array returned by open bytes? (Sorry for the noob questions, I'm extremely new to this, and have never worked with complex image types)
Maybe someone else can clarify further; sleepy time for me.
bpp is the bytes per pixel, fp is a boolean representing if the data is floating point or not. The return type of values in the array received back is based on these 2 values
If the bytes per pixel == 1 then your return array will be a byte[][]
If the bytes per pixel == 2 then your return array will be a short[][]
If the bytes per pixel == 4 and floating point then your return array will be a double[][]