From 7d52e6dadd3dcc4a05d8e3b7563cb217e6a4a38d Mon Sep 17 00:00:00 2001 From: AnniekStok Date: Tue, 1 Oct 2024 09:10:52 +0200 Subject: [PATCH] Add activity to open TIF image in ImageJ gui, #720 --- _includes/image_file_formats/open_tif.md | 8 ++++++++ _includes/image_file_formats/open_tif_imagejgui.md | 8 ++++++++ _modules/image_file_formats.md | 3 ++- 3 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 _includes/image_file_formats/open_tif.md create mode 100644 _includes/image_file_formats/open_tif_imagejgui.md diff --git a/_includes/image_file_formats/open_tif.md b/_includes/image_file_formats/open_tif.md new file mode 100644 index 00000000..31b4eebd --- /dev/null +++ b/_includes/image_file_formats/open_tif.md @@ -0,0 +1,8 @@ +

Open TIF image data

+ +- 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 new file mode 100644 index 00000000..c35b4787 --- /dev/null +++ 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 index 02039efe..2c142e5a 100644 --- 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"]]]