[ome-users] Wrong metadata and slow performance with BigTiff

[Jan Eglinger]

Dear OME team,

I'd like to report two issues I noticed with reading and writing BigTIFF 
format with Bio-Formats:

  1) When using Bio-Formats Exporter in Fiji to write a z-stack to .btf, 
the dimensions get mixed up, z slices are becoming t frames

  2) Reading .btf is surprisingly much slower than writing, and the 
performance on Windows is almost 10-times worse than on Mac OSX, similar 
to another issue with reading OME-Tiff files on Windows:
   http://trac.openmicroscopy.org/ome/ticket/12930

To illustrate the issue, please use the attached macro code.

On Mac OSX, I get the following output:

   Before saving: 1000 slices, 1 frames
   Saving took 27907 ms
   Reading took 1132937 ms
   After saving: 1 slices, 1000 frames

On Windows, the output is:

   Before saving: 1000 slices, 1 frames
   Saving took 224195 ms
   Reading took 10899405 ms
   After saving: 1 slices, 1000 frames

I used an up-to-date Fiji with 64-bit Java 1.6.0 on both OSX and Windows.


Jan
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file_name = "test.btf";
tmp = getDirectory("temp");
newImage("BigTIFF_test", "8-bit black", 1000, 1000, 1000);
getDimensions(w, h, c, slices_before, frames_before);
print("Before saving: " + slices_before + " slices, " + frames_before + " frames");
tic = getTime();
run("Bio-Formats Exporter", "save=" + tmp + file_name +" compression=Uncompressed");
tac = getTime();
print("Saving took " + (tac-tic) + " ms");
run("Bio-Formats Importer", "open=" + tmp + file_name +" color_mode=Default view=Hyperstack stack_order=XYCZT");
toc = getTime();
print("Reading took " + (toc-tac) + " ms");

getDimensions(w, h, c, slices_after, frames_after);
print("After saving: " + slices_after + " slices, " + frames_after + " frames");