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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # BioImage-Analysis-and-Data-Processing-Workshop-2024
 This repository hosts material for the BioImage Analysis and Data Processing Workshop 2024, which takes place in VMCF Microscopy Facility, Vinicna 7, Prague, Czechia
 
-This repository hosts the workshop' jupyter notebooks and slides.
+This repository hosts the workshop' jupyter notebooks, markdown files and slides.
 
 This work is licensed by the Bio-Image Analysis Technology Development group (BiAPoL), Cluster of Excellence Physics of Life (PoL), Dresden, under a Creative Commons Attribution 4.0 International License.
 It contains derived materials from previous work from Robert Haase (ScaDS AI Leipzig), Johannes Soltwedel (PoL Dresden), Till Körten (Helmholtz AI Dresden) and Guillaume Witz (Universität Bern).

diff --git a/data/BBBC007_batch/A9 p7d.tif b/data/BBBC007_batch/A9 p7d.tif
diff --git a/data/BBBC007_batch/AS_09125_040701150004_A02f00d0.tif b/data/BBBC007_batch/AS_09125_040701150004_A02f00d0.tif
diff --git a/data/BBBC007_cropped/images/A9 p5d (cropped 1).tif b/data/BBBC007_cropped/images/A9 p5d (cropped 1).tif
diff --git a/data/BBBC007_cropped/images/A9 p5d (cropped 2).tif b/data/BBBC007_cropped/images/A9 p5d (cropped 2).tif
diff --git a/data/BBBC007_cropped/images/A9 p5d (cropped 3).tif b/data/BBBC007_cropped/images/A9 p5d (cropped 3).tif
diff --git a/data/BBBC007_cropped/images/A9 p5d (cropped 4).tif b/data/BBBC007_cropped/images/A9 p5d (cropped 4).tif
diff --git a/data/BBBC007_cropped/masks/A9 p5d (cropped 3).tif b/data/BBBC007_cropped/masks/A9 p5d (cropped 3).tif
diff --git a/data/BBBC007_cropped/masks/A9 p5d (cropped 4).tif b/data/BBBC007_cropped/masks/A9 p5d (cropped 4).tif
diff --git a/data/BBBC007_data_source.txt b/data/BBBC007_data_source.txt
diff --git a/data/BBBC007_reference.txt b/data/BBBC007_reference.txt
@@ -0,0 +1,2 @@
+"We used image set BBBC007v1 image set version 1 (Jones et al., Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, 2005), available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."
+The images "17P1_POS0006_D_1UL.tif" and "17P1_POS0006_F_2UL.tif" were cropped (square 220px large with upper-left corner positioned at [80px, 150px] [x, y]) and converted from RGB to 16bit depth.
diff --git a/data/BMP4blastocystC3-cropped_resampled_8bit.tif b/data/BMP4blastocystC3-cropped_resampled_8bit.tif
diff --git a/data/BMP4blastocystC3-cropped_resampled_8bit_2nuclei.tif b/data/BMP4blastocystC3-cropped_resampled_8bit_2nuclei.tif
diff --git a/data/BMP4blastocystC3-cropped_resampled_8bit_image_data_source.txt b/data/BMP4blastocystC3-cropped_resampled_8bit_image_data_source.txt
diff --git a/data/C2C12_Nuclei.tif b/data/C2C12_Nuclei.tif
diff --git a/data/human_mitosis_noisy.tif b/data/human_mitosis_noisy.tif
diff --git a/data/multichannel/actin.tif b/data/multichannel/actin.tif
diff --git a/...C007_cropped/masks/A9 p5d (cropped 1).tif → data/multichannel/cell_labels.tif b/...C007_cropped/masks/A9 p5d (cropped 1).tif → data/multichannel/cell_labels.tif
diff --git a/data/multichannel/dna.tif b/data/multichannel/dna.tif
diff --git a/...C007_cropped/masks/A9 p5d (cropped 2).tif → data/multichannel/dna_labels.tif b/...C007_cropped/masks/A9 p5d (cropped 2).tif → data/multichannel/dna_labels.tif
diff --git a/data/nuclei/nuclei3d.tif b/data/nuclei/nuclei3d.tif
diff --git a/data/nuclei/nuclei3d_cropped.tif b/data/nuclei/nuclei3d_cropped.tif
diff --git a/data/nuclei/outputs/largest_surface_nuclei3d.stl b/data/nuclei/outputs/largest_surface_nuclei3d.stl
diff --git a/data/nuclei/outputs/largest_surface_nuclei3d_cropped.stl b/data/nuclei/outputs/largest_surface_nuclei3d_cropped.stl
diff --git a/data/nuclei/outputs/segmentation_results_nuclei3d.tif b/data/nuclei/outputs/segmentation_results_nuclei3d.tif
diff --git a/data/nuclei/outputs/segmentation_results_nuclei3d_cropped.tif b/data/nuclei/outputs/segmentation_results_nuclei3d_cropped.tif
diff --git a/data/nuclei/outputs/table_nuclei3d.csv b/data/nuclei/outputs/table_nuclei3d.csv
diff --git a/data/nuclei/outputs/table_nuclei3d_cropped.csv b/data/nuclei/outputs/table_nuclei3d_cropped.csv
diff --git a/data/zfish_eye.tif b/data/zfish_eye.tif
diff --git a/data/zfish_eye_source.txt b/data/zfish_eye_source.txt
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/00_intro.md b/docs/BioImage_Analysis_with_Jupyter_and_napari/00_intro.md
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/02_Napari_from_Jupyter_introduction.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/02_Napari_from_Jupyter_introduction.ipynb
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/03_Filters_in_3D_Isotropic_Data.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/03_Filters_in_3D_Isotropic_Data.ipynb
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/04_Brightness_and_Contrast_optional.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/04_Brightness_and_Contrast_optional.ipynb
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/05_Filters_optional.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/05_Filters_optional.ipynb
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/06_Segmentation_workflow_example.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/06_Segmentation_workflow_example.ipynb
diff --git a/docs/BioImage_Analysis_with_Jupyter_and_napari/07_batch_segmentation_workflow_example.ipynb b/docs/BioImage_Analysis_with_Jupyter_and_napari/07_batch_segmentation_workflow_example.ipynb
diff --git a/docs/Machine_Learning_with_napari/00_intro.md b/docs/Machine_Learning_with_napari/00_intro.md
diff --git a/docs/Machine_Learning_with_napari/apoc_train_on_folders.ipynb b/docs/Machine_Learning_with_napari/apoc_train_on_folders.ipynb
diff --git a/docs/Program Idea.docx b/docs/Program Idea.docx
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -7,26 +7,12 @@ root: intro
 options: # The options key will be applied to all chapters, but not sub-sections
   numbered: False
 
-parts:
-- caption: Bio-Image Analysis with Jupyter and napari
-  chapters:
-  - file: BioImage_Analysis_with_Jupyter_and_napari/00_intro
-    sections:
-    - file: BioImage_Analysis_with_Jupyter_and_napari/01_images_are_numpy_arrays
-    - file: BioImage_Analysis_with_Jupyter_and_napari/02_Napari_from_Jupyter_introduction
-    - file: BioImage_Analysis_with_Jupyter_and_napari/03_Filters_in_3D_Isotropic_Data
-    - file: BioImage_Analysis_with_Jupyter_and_napari/04_Brightness_and_Contrast_optional
-    - file: BioImage_Analysis_with_Jupyter_and_napari/05_Filters_optional
-    - file: BioImage_Analysis_with_Jupyter_and_napari/06_Segmentation_workflow_example
-    - file: BioImage_Analysis_with_Jupyter_and_napari/07_batch_segmentation_workflow_example
-    - file: BioImage_Analysis_with_Jupyter_and_napari/08_napari-assistant
-    - file: BioImage_Analysis_with_Jupyter_and_napari/09_notebook_export
-- caption: Machine Learning with napari Plugins
-  chapters:
-  - file: Machine_Learning_with_napari/00_intro
-    sections:
-    - file: Machine_Learning_with_napari/interactive_pixel_classification/readme
-    - file: Machine_Learning_with_napari/interactive_object_classification/readme
-    - file: Machine_Learning_with_napari/apoc_train_on_folders
-    - file: Machine_Learning_with_napari/interactive_unsupervised_object_classification/readme
-    - file: Machine_Learning_with_napari/FLIM/readme
+chapters:
+- file: napari_workshop/01_images_are_numpy_arrays
+- file: napari_workshop/08_napari-assistant
+- file: napari_workshop/09_notebook_export
+- file: napari_workshop/multichannel_analysis/readme
+- file: napari_workshop/interactive_pixel_classification/readme
+- file: napari_workshop/interactive_object_classification/readme
+- file: napari_workshop/interactive_unsupervised_object_classification/readme
+- file: napari_workshop/FLIM/readme
diff --git a/docs/images/export_notebooks05.jpg b/docs/images/export_notebooks05.jpg
diff --git a/docs/images/export_notebooks08.jpg b/docs/images/export_notebooks08.jpg
diff --git a/docs/installation.md b/docs/installation.md