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The beginning
BiAPoL · Aug 6, 2024 · 153be55 · 153be55
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diff --git a/README.md b/README.md
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-# QM Course Lectures on Bio-Image Analysis with napari 2024
-QM course lectures about bio-image analysis using napari taught at VMCF, Charles University in Prague, March 2024.
+# 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 lectures' jupyter notebooks and slides.
+This repository hosts the workshop' jupyter notebooks, markdown files and slides.
 
-This work is licensed by Marcelo Leomil Zoccoler, PoL Dresden, under a Creative Commons Attribution 4.0 International License.
+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).
 
-The Jupyter book of the course can be viewed under this URL: https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_2024/intro.html
+The Jupyter book of the course can be viewed under this URL: **to be added**
 
 It is maintained using [Jupyter lab](https://jupyter.org/) and build using [Jupyter book](https://jupyterbook.org/en/stable/intro.html).
 
 ## Acknowledgements
 
-I would like to thank all people who made previous contributions to this work and to Zuzana Burdíková and Martin Schätz (Charles University Prague) for the invitation to give these lectures.
+I would like to thank all people who made previous contributions to this work and, in particular, to Zuzana Burdíková and Martin Schätz (Charles University Prague) for the invitation to give this workshop.
 
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
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+"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