Viz: image stack as animated GIF

[JohnTigue]

Demo: datatset_get_eyes_on_image_stack.ipynb

To do

• Get minimally working
• MinIP as slide 0 i.e. the preview. What people see before animation. Use libgif
• MinIP as last slide. This way after playing, MinIP is left on the screen.
• Get Colab to play animation.
• Add progress bar to bottom of each image, showing depth of stack

Goal, animated GIF of stack i.e. all images into a single GIF. This is an initial "eyes on data" thing, which does not involve any automated reconstructions, just visualizing the input dataset.

The Brightfield Challenge dataset is basically just a raw z-stack of 2D images, plus SWC files. This project seeks to explore "doing neuroscience on Colab." So, crank out some code that does basic image processing on the image stack

Each neuron has an image stack.

The whole image stack is on the order of 6 to 60 GB
Each stack has a few hundred images
Each image file is on the order of 10s of MB each
So, how about "compress" the image stack into an animated GIF file of no more than a few MB, for easy viewing over the web? Looks like ImageJ already does this. That's Java; would be nice to find a Python implementation.

[JohnTigue]

Possibly useful:

• Extracting The Frames Of An Animated GIF Using Pillow
• making gif from images using imageio in python

[JohnTigue]

Still need to figure out how to get the animated gif to show in the notebook. As is need to download and embed in an HTML page. Unacceptable.

Embedding Matplotlib Animations in Jupyter Notebooks
Louis Tiao 2016-04-16 21:10 11 Comments Source (2016):

UPDATE (March 2018): For a more modern solution that uses an interactive JavaScript widget, please go to my new post: Embedding Matplotlib Animations in Jupyter as Interactive JavaScript Widgets.

Embedding Matplotlib Animations in IPython Notebooks is the original article referenced.

[JohnTigue]

Various techniques to control animated gif

• handcoded: preloading
• libgif and x-gif: ping-pong
• libgif: rubbable, progress-bar, play/pause and move_to() means can make like a movie i.e. paused movie with draggable time slider equals z-stack explorer.

Pre-caching:

<script type="text/javascript">
  (new Image()).src = "animatedgif.gif"; // this would preload the GIF, so future loads will be instantaneous
</script>

[JohnTigue]

PIL.Image and animated gif:
https://stackoverflow.com/questions/7960600/python-tkinter-display-animated-gif-using-pil

canvas = Image.new("RGB",(Width,Height),"white")
gif = Image.open('text.gif', 'r')
frames = []
try:
    while 1:
        frames.append(gif.copy())
        gif.seek(len(frames))
except EOFError:
    pass

for frame in frames:
     canvas.paste(frame)
     canvas.show()

[JohnTigue]

Save Matplotlib Animations as GIFs