When trying to load OME-TIFF files generated from e.g. FIJI, I can't seem to get the VolumeViewer to display the data correctly in the dev server example.
I generated a sample 3-channel 8-bit image stack (200x200x200 pixels) with a single time point, and saved the resultant data using both the "standard" OME-TIFF exporter in FIJI and also using the Bio-Formats exporter plugin.
In both cases, Volume Viewer appears to read the file correctly (three channels show up in the UI drawers) but only the first channel is actually displayed (in purple). I can't seem to get the other channels to display.
I tried this by simply modifying the index.ts file to put a URL to my generated file(s) under the omeTIFF entry in the TEST_DATAmap, while keeping the type unchanged (VolumeFileFormat.TIFF).
I also tried with a single-channel OME-TIFF file generated in FIJI, and although VolumeViewer appears to load the data and understand that it's a single-channel OME-TIFF file ... I don't see any visual output.
Expected Behavior
I'd expect all the channel data in the 3- or 1-channel OME-TIFF files to display, as they do for e.g. the AICS-12_881.ome.tif file specified in the original test data map.
Reproduction
Run FIJI and use File -> New -> Hyperstack. Specify 8-bit and e.g. 200x200x200 pixels with 3 channels and one "Frames" (i.e., timepoints). Ensure "Label imges" is selected. Then save the resultant data as OME-TIFF via File -> Save as -> OME-TIFF or Plugins -> Bio-Formats -> Bio-formats Exporter
Environment
FIJI 1.54f
VolumeViewer 3.8.3 dev (via cloning GitHub repo and npm dev run)
Description
When trying to load OME-TIFF files generated from e.g. FIJI, I can't seem to get the VolumeViewer to display the data correctly in the dev server example.
I generated a sample 3-channel 8-bit image stack (200x200x200 pixels) with a single time point, and saved the resultant data using both the "standard" OME-TIFF exporter in FIJI and also using the Bio-Formats exporter plugin.
In both cases, Volume Viewer appears to read the file correctly (three channels show up in the UI drawers) but only the first channel is actually displayed (in purple). I can't seem to get the other channels to display.
I tried this by simply modifying the
index.tsfile to put a URL to my generated file(s) under theomeTIFFentry in theTEST_DATAmap, while keeping the type unchanged (VolumeFileFormat.TIFF).I also tried with a single-channel OME-TIFF file generated in FIJI, and although VolumeViewer appears to load the data and understand that it's a single-channel OME-TIFF file ... I don't see any visual output.
Expected Behavior
I'd expect all the channel data in the 3- or 1-channel OME-TIFF files to display, as they do for e.g. the
AICS-12_881.ome.tiffile specified in the original test data map.Reproduction
Run FIJI and use
File -> New -> Hyperstack. Specify 8-bit and e.g. 200x200x200 pixels with 3 channels and one "Frames" (i.e., timepoints). Ensure "Label imges" is selected. Then save the resultant data as OME-TIFF viaFile -> Save as -> OME-TIFForPlugins -> Bio-Formats -> Bio-formats ExporterEnvironment
FIJI 1.54f VolumeViewer 3.8.3 dev (via cloning GitHub repo and
npm dev run)