diff --git a/README.md b/README.md index c5f0345..f8ea9ff 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,6 @@ __Drag-and-drop__ visualisation of outputs from `looptrace` This package is a plugin for [Napari](https://napari.org/stable/) to facilitate interactive viewing of various results from [`looptrace`](https://github.com/gerlichlab/looptrace). ## Guides and documentation -Included is, among other things, documentation about [what's viewable](./docs/user_docs/README.md#what-can-be-visualised) with this plugin, how to [get started](./docs/user_docs/README.md#quickstart) using this plugin, or how to [develop](./docs/development.md) this plugin. +Included are, among other things, documentation about [what's viewable](./docs/user_docs/README.md#what-can-be-visualised) with this plugin, how to [get started](./docs/user_docs/README.md#quickstart) using this plugin, and how to [develop](./docs/development.md) this plugin. -Here's the ["home" of the documentation](./docs/). +Here's the [documentation "home"](./docs/). diff --git a/docs/development.md b/docs/development.md index 84c71a5..08797ab 100644 --- a/docs/development.md +++ b/docs/development.md @@ -1,6 +1,7 @@ ## Development This project uses a Nix shell to provide a development environment. To develop on this plugin, please ensure first that you have [installed the Nix package manager](https://nixos.org/download/), ideally, or that you have all the dependencies you'll need otherwise installed (e.g., in a virtual environment you're managing separately). +If you're using the Nix shell, the first time it's started it will create a `.venv` subfolder in the project root folder. By default, with `nix-shell`, you should have all the dependencies you'll need not only to _use_ this plugin, but also to _develop_ on it. In other words, dependencies to do things like run tests, run linter(s), and run type checking should all be provided. @@ -10,7 +11,7 @@ If an issue's open for what you're experiencing, please upvote the initial descr ### Testing, formatting, and linting Here's what corresponds approximately to what's run for CI through the project's [GitHub actions workflows](../.github/workflows/). -NB: Each of the following commands is to be run _from the project [root folder](../)_. +NB: Each of the following commands is to be run _from the project [root folder](../)_, typically from the project's Nix shell. __Run test suite__ with coverage statistics ```console @@ -32,4 +33,4 @@ mypy looptrace_napari __Run linter__ ```console pylint looptrace_napari -``` \ No newline at end of file +``` diff --git a/docs/user_docs/locus-spots.md b/docs/user_docs/locus-spots.md index 4dfd321..76cd15f 100644 --- a/docs/user_docs/locus-spots.md +++ b/docs/user_docs/locus-spots.md @@ -1,4 +1,4 @@ -## Locus spots visualisations +## Viewing locus spots ### Quickstart To visualise the locus-specific spots masks, you need to __drag-and-drop files__ into an active Napari window. @@ -10,9 +10,8 @@ To visualise the locus-specific spots masks, you need to __drag-and-drop files__ ### What you should see A Napari window with a three sliders and three layers (QC pass, QC fail, and pixel data). - Bottom slider: ROI/trace -- Middle slider: -- Top slider: - +- Middle slider: imaging timepoint +- Top slider: slice in `z` ### Details and troubleshooting __Scrolling__ diff --git a/docs/user_docs/nuclear-masks.md b/docs/user_docs/nuclear-masks.md index e6653ed..eb79ad6 100644 --- a/docs/user_docs/nuclear-masks.md +++ b/docs/user_docs/nuclear-masks.md @@ -1,4 +1,4 @@ -## Nuclear masks visualisation +## Viewing nuclear masks First, check the [general quickstart](./README.md#quickstart), ensuring you have an environment ready to go. ### Quickstart @@ -11,7 +11,7 @@ That folder must... * `nuc_masks`: "images" (2D), encoding the subregions of each image deemed to be nuclei. 0 a non-nuclear pixel while positive integer indicates membership of the pixel in a particular nucleus (corresponding to a `label` value in the corresponding points/labels file for the particular field of view in question). * `_nuclear_masks_visualisation`: table-like files (CSV), for now, with a `label` column indicating _which_ nucleus a record represents, and `yc` and `xc` columns giving y- and x-coordinates, respectively, for the centroid of a particular nuclear region. -These properties should be nearly satisfied a run of `looptrace`. +These properties should be nearly satisfied by a run of `looptrace`. Perhaps only these steps will be required to prepare the data: 1. Copy the nuclear mask visualisation folder (with the points/labels file(s)) into a shared folder with the nuclei images and masks. 1. Add an underscore as prefix to the name of the copy of the folder. @@ -25,7 +25,7 @@ The fields of view displayed will be those for which all three files (image, mas * Each relevant file, regardless of which kind of data are inside, should have a basename like `PXXXX`, where `XXXX` corresponds to the 1-based integer index of the field of view, left-padded with zeroes, e.g. P0001. * Each image or masks file should have a `.zarr` extension. * Each points/labels file should have a `.nuclear_masks.csv` extension. -* Each `.zarr` should either have a `.zarray` immediately inside it, or a single `0` subfolder which has a `.zarray` inside it. +* Each `.zarr` should either have a `.zarray` immediately inside it, or have a single `0` subfolder which has a `.zarray` inside it. * In general, you probably want the fields of view to match up among the three types of files involved (images, masks, points/labels), and to be numbered $1, 2, ..., N$, $N$ being the number of fields of view in your experiment (or whatever subset of the experiment you want to visualise). * Each image or masks ZARR should in general be 2D or 5D, each of the first three axes having length 1 if 5D. * Each points/labels file should have first column unnamed, just as row index; other columns should be `label` (unique per row, natural numbers), then `yc` and `xc` as nonnegative real numbers giving 2D coordinates of nucleus center.