docs tweaks

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/).

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
-```
+```

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__

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.