id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1773	Optimize speed reading TIFF volume data	Tom Goddard	Tom Goddard	"Reading 3d images in TIFF format with Pillow is much slower than one would expect based on disk I/O speed.  It is possible to increase the read speed perhaps 5-fold using something other than Pillow.

I used an example image AICS-10_10.ome.tif, 390 Mbytes, grid size 1024 by 1024 by 81, 16-bit grayscale values, 8 channels (3 wavelengths, one brightfield, 4 segmentations).  This file would normally be 1.3 Gbytes but deflate compression is being used.  Four channels are binary (0/1) segmentations that compress to very small size.  The three fluorophore channels use only about 8-bits for most data values.  Decompressing the data is part of the time of reading the file.

Timings reading AICS-10_10.ome.tif, only first 3 channels.

  7.3 seconds -  ChimeraX open at step 2 then switch to step 1, includes blending and graphics.
  5.2 seconds - Pillow 5.4.1 with standalone script reading planes for 3 channels.
  1.8 seconds - libtiff C program reading planes for 3 channels and making single 3d array
  0.8 seconds - tiffile.py single Python script reading all planes of first 3 channels

The tifffile.py library is in PyPi, seems well maintained, and is specifically for optical microscopy.  Seems like a good choice to replace Pillow.
"	enhancement	closed	moderate		Volume Data		fixed						all	ChimeraX