Add activity to open TIF image in ImageJ gui, #720

NEUBIAS · Oct 1, 2024 · 7d52e6d · 7d52e6d
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diff --git a/_includes/image_file_formats/open_tif.md b/_includes/image_file_formats/open_tif.md
@@ -0,0 +1,8 @@
+<h4 id="open_tif"><a href="#open_tif">Open TIF image data</a></h4>
+
+- Open a TIF (Tag Image File) file and inspect its pixel and metatdata content
+
+##### Data
+
+- [TIF image file (minimal metadata)](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_PLK1_control.tif)
+- [TIF image file (extensive metadata)](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_16bit__collagen.md.tif)
diff --git a/_includes/image_file_formats/open_tif_imagejgui.md b/_includes/image_file_formats/open_tif_imagejgui.md
@@ -0,0 +1,8 @@
+- Open the file mentioned in the activity by drag and drop into the FIJI window:
+  - Inspect the image
+  - Inspect the metadata via [Image > Show info...]
+- Close the image and open it again via Bio-Formats Importer:
+  - [Plugins > Bio-Formats > Bio-Formats Importer]
+  - Select your image
+  - [X] Display metadata
+  - Click [OK]
diff --git a/_modules/image_file_formats.md b/_modules/image_file_formats.md
@@ -25,10 +25,11 @@ concept_map: >
     MD --> DS("Display settings")
     MD --> NA("...")
 
-figure: /figures/image_file_formats.png 
+figure: /figures/image_file_formats.png
 figure_legend: "Image pixel data are saved as binary data on disk. Essential metadata is needed to load the binary data into an image array."
 
 multiactivities:
+  - ["image_file_formats/open_tif.md", [["ImageJ GUI", "image_file_formats/open_tif_imagejgui.md"],["python BioIO", "image_file_formats/open_tif_bioio.py"]]]
   - ["image_file_formats/open_czi.md", [["ImageJ GUI", "image_file_formats/open_czi_imagejgui.md"],["python BioIO", "image_file_formats/open_czi_bioio.py"]]]
   - ["image_file_formats/open_em_tiff_series.md", [["ImageJ GUI", "image_file_formats/open_em_tiff_series_imagejgui.md"],["python BioIO", "image_file_formats/open_em_tiff_series_bioio.py"]]]
   - ["image_file_formats/open_diverse_file_formats.md", [["ImageJ GUI", "image_file_formats/open_diverse_file_formats_imagejgui.md"],["python BioIO", "image_file_formats/open_diverse_file_formats_bioio.py"]]]