Merge branch 'master' of https://github.com/NEUBIAS/training-resources

courses/2024_manual_image_measurements.md

@@ -38,13 +38,16 @@ Scientists that may use microscopy data in their research.
 ### 9:30 - 12:30 (including break)
 
 1. [Manual shape measurements](https://neubias.github.io/training-resources/measure_shapes/index.html)
-    - TODO (Tischi): Improve the figure, i.e. add manual ROIs, remove the binary, make the cc image coloured (like in the measure_intensities module)
-    - TODO (Tischi): Add manual IJ GUI shape 2D measurements activity, teach that one can save the ROIs!
-    - TODO (???): Add manual IJ GUI 3D spots counting (multi-point ROI)
+    - DONE (Tischi): Improve the figure, i.e. add manual ROIs, remove the binary, make the cc image coloured (like in the measure_intensities module)
+    - DONE (Tischi): Add manual IJ GUI shape 2D measurements activity, teach that one can save the ROIs!
+    - TODO (Arif?): Add manual IJ GUI 3D spots counting (multi-point ROI)
+1. [Fluorescence image formation](https://neubias.github.io/training-resources/image_formation_confocal/index.html)
+    - DONE (Tischi): Module is still a draft
+    - DONE (Tischi): Add activity, using this image: xyzc_8bit__zebrafish_HisGFP_LyntdTomato.tif
 1. [Manual intensity measurements](https://neubias.github.io/training-resources/measure_intensities/index.html)
     - DONE (Tischi): Add ROIs for the nuclei in the figure 
     - DONE (Tischi): Add ImageJ GUI manual ROI 2D intensity measurement activity
-    - TODO (Tischi) Using the image formation example data Add ImageJ GUI manual 2D ROI intensity measurement in a 3D tissue culture image, either in a single slice or sum projection, in a widefield and in confocal image
+    - TODO (Tischi?) Using the image formation example data add ImageJ GUI manual 2D ROI intensity measurement in a 3D tissue culture image, either in a single slice or sum projection, in a widefield and in confocal image
 1. [Manual 3D object delineation](https://neubias.github.io/training-resources/manual_segmentation/index.html)
     - TODO (Arif?): make this module work
     - ...one could then use the 3D ROI manager in Fiji to measure stuff (3D image suite)

courses/2024_scientific_image_inspection_and_presentation.md

@@ -45,7 +45,7 @@ Scientists that may use microscopy data in their research.
 1. [Image file formats](https://neubias.github.io/training-resources/image_file_formats/index.html)
 1. [Scientfic image data presentation](https://neubias.github.io/training-resources/image_inspection_and_presentation/index.html)
     - Now we are ready to perform the module activity and create the scientific image presentation
-    - TODO the activity needs to be adapted: https://github.com/NEUBIAS/training-resources/issues/606 
+    - TODO the activity needs to be adapted: https://github.com/NEUBIAS/training-resources/issues/606  (ARIF)
 
 ### Timing
 

courses/2024_volumetric_image_inspection_and_presentation.md

@@ -38,14 +38,11 @@ Scientists that may use microscopy data in their research.
 ### 9:30 - 11:30 (including break)
 
 1. [Volume slicing](https://neubias.github.io/training-resources/volume_slicing/index.html)
-   - TODO (Tischi): https://github.com/NEUBIAS/training-resources/issues/613
-1. [Confocal image formation](https://neubias.github.io/training-resources/image_formation_confocal/index.html)
-    - TODO (Tischi): Module is still a draft
-    - TODO (Tischi): Add activity, using this image: xyzc_8bit__zebrafish_HisGFP_LyntdTomato.tif
+   - DONE (Tischi): https://github.com/NEUBIAS/training-resources/issues/613
 1. [Projections](https://neubias.github.io/training-resources/projections/index.html)
 1. [Volume rendering](https://neubias.github.io/training-resources/volume_viewer/index.html)
-    - TODO: Check which viewer we want to use for this; maybe Napari?
-    - TODO: Can one just install napari as a standalone App, without conda?
+    - TODO (Arif): Check which viewer we want to use for this; maybe Napari?
+    - TODO (Arif): Can one just install napari as a standalone App, without conda?
 
 ### 11:30 - 12:30