pyqtGraph to display a .tif stack

This will display a 3D .tif stack where slices can be viewed and contrast set.

Install libraries

pip install pyqtgraph
pip install tifffile

Python code

import pyqtgraph as pg
import tifffile
tif = tifffile.TiffFile('Desktop/zyF4107_d1_s0_ch1.tif')
images = tif.asarray()
pg.image(images)

To Do

• Not sure how this works for 2 channels.
• See how easy it is to plugin custom python code into PyQtGraph.
  1. Remove the right contrast slider and bottom slice slider.
  2. Swap mouse wheel from zooming image to scrolling slices.
  3. Overlay 3D annotations that are masked. Appear and disappear as a function of slices.
  4. Select a 3D annotation.

Links

• PyQtGraph
• TiffFile is provided by Christoph Gohlke and is here