Getting started#
Five short tutorials that take you from an unopened microscopy file to a growth-rate curve. They are meant to be read in order — each one builds on the last.
Every tutorial is a real Jupyter notebook. Click the Colab badge at the top of
any of them to run it in your browser with nothing installed, or find them under
docs/tutorials/ in the repository.
One function for ND2, CZI, TIFF stacks and folders of TIFFs. Read metadata without loading pixels, and pull out a position as a time series.
The (T, H, W, C) convention and numpy-style slicing — subsample, crop and pick
channels without copying a single pixel.
The interactive Jupyter viewer, contact sheets, scale bars, timestamps, and exporting an annotated video.
Declare pixel size and frame interval once, and get results in µm² and hours instead of px² and frames.
The payoff: deep-learning segmentation, measurement, artefact filtering and a population growth rate — on real data, GPU optional.
Before you start, make sure acia is installed — see Installation. The
notebooks install it themselves if you run them on Colab.