-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Viz: image stack as animated GIF #20
Comments
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
Embedding Matplotlib Animations in IPython Notebooks is the original article referenced. |
Various techniques to control animated gif
Pre-caching:
|
PIL.Image and animated gif:
|
Demo: datatset_get_eyes_on_image_stack.ipynb
To do
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.
The text was updated successfully, but these errors were encountered: