From ba3730db7d8e792814d0579e3371f55164bb2321 Mon Sep 17 00:00:00 2001
From: Jordao Bragantini <jordao.bragantini@czbiohub.org>
Date: Thu, 17 Oct 2024 16:55:53 -0700
Subject: [PATCH] updated workflow and a bit of docs

---
 .github/workflows/pages.yml | 5 ++++-
 environment.yml             | 3 ++-
 requirements.txt            | 2 +-
 tutorial/installation.md    | 2 ++
 tutorial/tracking.md        | 9 +++++----
 5 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
index 0a3074f..e44bff2 100644
--- a/.github/workflows/pages.yml
+++ b/.github/workflows/pages.yml
@@ -20,6 +20,9 @@ concurrency:
   group: "pages"
   cancel-in-progress: true
 
+env:
+  TQDM_DISABLE: 1
+
 jobs:
   # Single deploy job since we're just deploying
   deploy:
@@ -43,7 +46,7 @@ jobs:
         with:
           run: |
             pip install -r requirements.txt
-            export TQDM_DISABLE=1; jupyter book build tutorial
+            jupyter book build tutorial
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
diff --git a/environment.yml b/environment.yml
index 7aea7ed..1115802 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,4 +23,5 @@ dependencies:
   - pip:
     - py-ctcmetrics
     - napari
-    - ultrack
+    - git+https://github.com/royerlab/ultrack
+    - napari-plot-profile
diff --git a/requirements.txt b/requirements.txt
index 8dd405d..192bdd9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,4 @@ napari-animation
 matplotlib
 py-ctcmetrics
 cellpose
-ultrack
+git+https://github.com/royerlab/ultrack
diff --git a/tutorial/installation.md b/tutorial/installation.md
index 190c67b..b1f4531 100644
--- a/tutorial/installation.md
+++ b/tutorial/installation.md
@@ -10,8 +10,10 @@ we will try to help you get unstuck.
 In this tutorial, we will install Python via miniforge, a distribution of
 Python based in the [conda package manager](https://docs.conda.io/en/latest/).
 
+```{note}
 If you already have anaconda, miniconda, or miniforge installed, those will work
 as well and you can skip to the bottom of this page to set up the conda environment.
+```
 
 1. In your web browser, navigate to the
    [miniforge page](https://github.com/conda-forge/miniforge). 
diff --git a/tutorial/tracking.md b/tutorial/tracking.md
index 7cc1fbf..9ff56bf 100644
--- a/tutorial/tracking.md
+++ b/tutorial/tracking.md
@@ -4,7 +4,7 @@ jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: 1.0.4
+    format_version: 0.13
     jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3 (ipykernel)
@@ -14,9 +14,11 @@ kernelspec:
 
 # 2D cell tracking with multiple hypotheses
 
++++
+
 This tutorial shows Ultrack's multiple hypotheses tracking capabilities. 
 
-Here, rather than searching for an optimal segmentation parameter, we sampled multiple segmentations with different parametrizations and used Ultrack to find the best segments, obtaining more accurate cell tracking.
+We will start with a simple classical image processing solution with ultrack and tracking cells for image intensities directly. Then, we will progress to using Cellpose and finally use multiple Cellpose segmentations to improve tracking performance without training our own segmentation model showcasing the improvement when a single segmentation isn't good enough.
 
 ## Download data
 
@@ -24,8 +26,7 @@ Download the Fluo-C2DL-Huh7 dataset from the [Cell Tracking Challenge](celltrack
 
 The dataset will be used for demonstrating the segmentation and tracking workflow.
 
-
-```{code-cell} python
+```{code-cell} ipython3
 :tags: [remove-output]
 
 !wget -nc http://data.celltrackingchallenge.net/training-datasets/Fluo-C2DL-Huh7.zip