Merge pull request #84 from BiAPoL/add-yolo-on-omero-tutorial

Add Yolo/OMERO tutorial
BiAPoL · Aug 20, 2024 · 1fb57d9 · 1fb57d9
2 parents c7e76f7 + 76d0ed2
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diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -7,6 +7,8 @@ parts:
 - caption: Blog Posts
   chapters:
   # Add new chapters here (recent first)
+  - file: johannes_mueller/yolo_from_omero/train_yolo
+  - file: mara_lampert/getting_started_with_miniforge_and_python/readme
   - file: stefan_hahmann/elephant_server_installation_windows/readme
   - file: stefan_hahmann/github_desktop_jupyter_notebook/readme
   - file: johannes_mueller/qtdesigner_and_magicgui/Readme

diff --git a/docs/images/yolo_dataset.PNG b/docs/images/yolo_dataset.PNG
diff --git a/docs/intro.md b/docs/intro.md
@@ -10,7 +10,12 @@ If you have feedback or suggestions, if spotted a typo, broken link or misleadin
 
 ## Recent blog posts
 
-### [Getting started with Miniforge and Python](mara_lampert/getting_started_with_miniforge_and_python/readme)
+### [Training a yolo model on an OMERO dataset](ref:yolo_omero)
+
+<small>[Johannes Soltwedel](johannes_mueller/readme), August 12th, 2024</small><br>
+<img src="images/yolo_dataset.PNG" width=10% align="right"><p>YOLO is a powerful tool for object detection and thus, obviously interesting in bio-image analysis. This blog post will show you how to train a YOLO model on an OMERO dataset.</p>
+
+### [Getting started with Miniforge and Python](mara_lampert/getting_started_with_miniforge_and_python/readme)]
 
 <small>[Mara Lampert](mara_lampert/readme), July 8th, 2024</small><br>
 <img src="images/package_manager.jpeg" width="100" align="right"><p>This post will help you to get started with Python using Miniforge. More precisely, you will learn how to install Miniforge, how to create and use conda environments and you will get to know some important packages for bio image analysis.</p>

diff --git a/docs/johannes_mueller/Readme.md b/docs/johannes_mueller/Readme.md
@@ -1,4 +1,4 @@
-# Johannes Müller
+# Johannes Soltwedel
 
 <img src="../images/johannes_mueller.jpg" alt="pol" width="150"/>
 
@@ -17,6 +17,7 @@ educate others to empower them to develop their own workflows and develop new me
 * [Advanced GUIs with Qt designer](entry_user_interf2/Readme)
 * [Automated package documentation with Sphinx](entry_sphinx/Readme)
 * [Getting started with Python and Anaconda](anaconda_getting_started/Readme)
+* [Training a yolo model on an OMERO dataset](ref:yolo_omero)
 
 ## Links
 * [BiA-PoL group website](https://physics-of-life.tu-dresden.de/en/research/technology-development-groups/bio-image-analysis)

diff --git a/docs/johannes_mueller/yolo_from_omero/detection.yaml b/docs/johannes_mueller/yolo_from_omero/detection.yaml
@@ -0,0 +1,10 @@
+path: E:/BiAPoL/yolo_demo/dataset  # dataset root dir
+train: train/images  # train images (relative to 'path') 128 images
+val: val/images  # val images (relative to 'path') 128 images
+test: test/images # test images (optional)
+
+names:
+  0: cell
+  1: compacted
+  2: spheroid
+  3: dead
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/PR_curve.png b/docs/johannes_mueller/yolo_from_omero/imgs/PR_curve.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/annotate.gif b/docs/johannes_mueller/yolo_from_omero/imgs/annotate.gif
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/confusion_matrix.png b/docs/johannes_mueller/yolo_from_omero/imgs/confusion_matrix.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/confusion_matrix_normalized.png b/docs/johannes_mueller/yolo_from_omero/imgs/confusion_matrix_normalized.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image1.png b/docs/johannes_mueller/yolo_from_omero/imgs/image1.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image2.PNG b/docs/johannes_mueller/yolo_from_omero/imgs/image2.PNG
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image3.PNG b/docs/johannes_mueller/yolo_from_omero/imgs/image3.PNG
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image4.PNG b/docs/johannes_mueller/yolo_from_omero/imgs/image4.PNG
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image5.png b/docs/johannes_mueller/yolo_from_omero/imgs/image5.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image6.png b/docs/johannes_mueller/yolo_from_omero/imgs/image6.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image7.png b/docs/johannes_mueller/yolo_from_omero/imgs/image7.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/image8.png b/docs/johannes_mueller/yolo_from_omero/imgs/image8.png
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/labels.jpg b/docs/johannes_mueller/yolo_from_omero/imgs/labels.jpg
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/train_batch0.jpg b/docs/johannes_mueller/yolo_from_omero/imgs/train_batch0.jpg
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/val_batch1_labels.jpg b/docs/johannes_mueller/yolo_from_omero/imgs/val_batch1_labels.jpg
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/val_batch1_pred.jpg b/docs/johannes_mueller/yolo_from_omero/imgs/val_batch1_pred.jpg
diff --git a/docs/johannes_mueller/yolo_from_omero/imgs/well_102_t0_x2671.34_y1437.11.png b/docs/johannes_mueller/yolo_from_omero/imgs/well_102_t0_x2671.34_y1437.11.png
diff --git a/docs/johannes_mueller/yolo_from_omero/train_yolo.ipynb b/docs/johannes_mueller/yolo_from_omero/train_yolo.ipynb
diff --git a/docs/mara_lampert/getting_started_with_miniforge_and_python/readme.md b/docs/mara_lampert/getting_started_with_miniforge_and_python/readme.md
@@ -1,3 +1,5 @@
+(ref:miniforge_python)=
+
 # Getting started with Miniforge and Python 
 [Mara Lampert](../readme), July 8th, 2024