Update guide-create-pyramids.md, index.md, and main-getting-started.md

docs/guide-create-pyramids.md

@@ -63,7 +63,7 @@ pyramidalize_directory("/path/to/your/images/", qupath_path="C:\Users\glegoc\App
     7. Go back to Parameters to choose the output directory and file prefix. "_s1", "_s2"... will be appended to the prefix.
     8. Back on the top, click the "Apply" button.
 
-The OME-TIFF files should be ready to be pyramidalized with the `create_pyramids.py` script.
+The OME-TIFF files should be ready to be pyramidalized with the `pyramid-creator` script.
 
 ## Usage
 See the instructions on the dedicated project page over at [Github](https://github.com/TeamNCMC/pyramid-creator#pyramid_creator).

docs/index.md

@@ -10,7 +10,7 @@ After [ABBA](https://abba-documentation.readthedocs.io/en/latest/) registration
 + compute metrics, such as objects density in each brain regions,
 + compute objects distributions in three three axes (rostro-caudal, dorso-ventral and medio-lateral),
 + compute averages and sem across animals,
-+ displaying all the above.
++ display all the above.
 
 This documentation contains `cuisto` [installation instructions](main-getting-started.md), ABBA [installation instructions](guide-install-abba.md), guides to [prepare images](guide-create-pyramids.md) for the pipeline, [detect objects](guide-qupath-objects.md) with QuPath, [register 2D slices on a 3D atlas](guide-register-abba.md) with ABBA, along with [examples](main-using-notebooks.md).
 

docs/main-getting-started.md

@@ -37,6 +37,12 @@ This is where you'll create QuPath projects, in which you'll be able to browse y
 This is the tool you'll use to register 2D histological sections to 3D atlases. See the [dedicated page](guide-install-abba.md).
 
 ### Python virtual environment manager (`conda`)
+
+!!! tip "TL;DR"
+
+    1. Install [Miniforge](https://conda-forge.org/download/), as user and adding to PATH.
+    2. Open a terminal (PowerShell in Windows) and run `conda init`
+
 The `cuisto` package is written in Python. It depends on scientific libraries (such as [NumPy](https://numpy.org/), [pandas](https://pandas.pydata.org/) and many more). Those libraries need to be installed in versions that are compatible with each other and with `cuisto`. To make sure those versions do not conflict with other Python tools you might be using (`deeplabcut`, `abba_python`, ...), we will install `cuisto` and its dependencies in a dedicated *virtual environment*.
 
 [`conda`](https://docs.conda.io/en/latest/) is a software that takes care of this. It comes with a "base" environment, from which we will create and manage other, project-specific environments. It is also used to download and install python in each of those environments, as well as third-party libraries. `conda` in itself is free and open-source and can be used freely by anyone.