# Acknowledgements

## The course

This module is taught by the **Single Cell Facility** of D-BSSE, ETH Zurich, as
part of the Lab Course *Methods in Cell Analysis and Laboratory Automation*.

A large part of the material derives, with permission, from teaching developed
over many years by **Aaron Ponti**, and from earlier editions of this course
prepared with **Andreas Cuny**. The `iaf` library that the homework relies on is
their work.

## The data

All example images come from the
**[Broad Bioimage Benchmark Collection](https://bbbc.broadinstitute.org/)**, a
public collection of annotated image sets maintained for exactly this kind of
use. Having expert annotations to compare against is what makes day 2 possible.

The collection as a whole should be cited as:

> Ljosa V, Sokolnicki KL, Carpenter AE (2012). *Annotated high-throughput
> microscopy image sets for validation.* Nature Methods 9(7):637.

The individual sets used here, with their source citations:

**[BBBC020](https://bbbc.broadinstitute.org/BBBC020)**: murine bone-marrow
derived macrophages, DAPI and CD11b. The guiding dataset for both days.

> "We used image set BBBC020 from the Broad Bioimage Benchmark Collection
> [Ljosa et al., Nature Methods, 2012]."

**[BBBC010](https://bbbc.broadinstitute.org/BBBC010)**: *C. elegans* live/dead
assay. Used for the detective game.

> "We used the *C. elegans* infection live/dead image set version 1 provided by
> Fred Ausubel and available from the Broad Bioimage Benchmark Collection
> [Ljosa et al., Nature Methods, 2012]."

**[BBBC030](https://bbbc.broadinstitute.org/BBBC030)**: Chinese hamster ovary
cells in DIC.

> "We used image set BBBC030v1 [Koos, K., Molnár, J., Kelemen, L., Tamás, G., &
> Horvath, P. (2016). *DIC image reconstruction using an energy minimization
> framework to visualize optical path length distribution.* Scientific Reports,
> 6.] from the Broad Bioimage Benchmark Collection."

Full provenance for every file, its source, the licence, and exactly what
processing was applied, is recorded in `data/MANIFEST.md`.

```{note}
The BBBC images are cropped and downscaled for teaching. If you use any of them
in your own work, go back to the originals: the versions here have been altered.
```

## The software

This course would not be possible without
[scikit-image](https://scikit-image.org/), [NumPy](https://numpy.org/),
[matplotlib](https://matplotlib.org/), [pandas](https://pandas.pydata.org/),
[SciPy](https://scipy.org/), [Fiji](https://fiji.sc/),
[Cellpose](https://www.cellpose.org/), [napari](https://napari.org/) and
[Jupyter](https://jupyter.org/).

If you rely on one of these tools in your own work, cite it to credit its
developers and maintainers.