From 4a4a5065a475656fcb56234d05f2997d9c0ef817 Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Wed, 7 Oct 2026 15:26:17 -0500 Subject: [PATCH 1/2] Update _toc.yml --- piximi-documentation/_toc.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/piximi-documentation/_toc.yml b/piximi-documentation/_toc.yml index 0bc669c..06d4b8f 100644 --- a/piximi-documentation/_toc.yml +++ b/piximi-documentation/_toc.yml @@ -4,6 +4,9 @@ parts: - caption: Quick Start chapters: - file: quick-start + - caption: Piximi Concepts + chapters: + - file: pages/detail/kinds-and-categories - caption: Piximi Views chapters: - file: pages/detail/projectviewer From d75c592584152ecccdaba52ea94f278e4a5989e3 Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Wed, 7 Oct 2026 15:39:07 -0500 Subject: [PATCH 2/2] Create kinds-and-categories.md --- .../pages/detail/kinds-and-categories.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 piximi-documentation/pages/detail/kinds-and-categories.md diff --git a/piximi-documentation/pages/detail/kinds-and-categories.md b/piximi-documentation/pages/detail/kinds-and-categories.md new file mode 100644 index 0000000..980e698 --- /dev/null +++ b/piximi-documentation/pages/detail/kinds-and-categories.md @@ -0,0 +1,19 @@ +# Kinds and Categories + +If using objects in Piximi, it's helpful to understand how Piximi groups objects, which are first into *kinds* and then into *categories*. + +## Kinds + +You can think of kinds as different, well, kinds of objects! A project where you are annotating tissue regions, cells, and nuclei could therefore have 3 "kinds" - one for regions, one for cells, and one for nuclei. Running a new segmentation model in Piximi will create a new "kind" automatically. All objects in a kind by default start off in the "Unknown" category. + +## Categories + +Categories are special in Piximi because they are the data structure that is used by the classifier - they let you break a "kind" of object (like cells) into multiple categories (like "MarkerAPositive" and "MarkerANegative"). If you want to train a deep learning classifier on objects in Piximi, it can only be for one "kind" at a time, so all objects must be the same kind but different categories. + +## How do I decide what's a kind and what's a category? + +Say I want to find all the cells in a field of view - some are mitotic and some are interphase. Should those be two different kinds or two different categories? + +It's really up to you! The most critical point is whether or not you want to identify all the objects together and sub-classify them using a deep learning classifier - in that case, you should make them all the same Kind and then make two Categories for "Mitotic" and "Interphase". + +If you aren't using the classifier, it mostly doesn't matter, but may vary by the segmentation approach you are taking - if the model you're using finds both kinds of things, you might as well treat them as the same kind and then just divide them into categories. If it only finds one of those groups well with a given set of segmentation settings (or annotation approaches), you might think about making them different kinds in two different segmentation passes. Neither option is wrong if you aren't using the classifier!