diff --git a/_includes/datatypes/metadata_and_datatype_imagej_gui.md b/_includes/datatypes/metadata_and_datatype_imagej_gui.md index 30bdc8bf..b716f8c4 100644 --- a/_includes/datatypes/metadata_and_datatype_imagej_gui.md +++ b/_includes/datatypes/metadata_and_datatype_imagej_gui.md @@ -7,4 +7,7 @@ For any image mentioned in the activity perform the below tasks. - Metadata: look for `SignificantBits` and `Type` - Check the maximum value in the image, e.g. using `Analyze > Histogram` - How does this maximum value compare the image's datatype? - - For example, you may find a value of 4095, which is the maximum of an unsigned integer 12 bit image, which may be the datatype mentioned in the image metadata, however ImageJ may represent this image as a 16 bit image. Appreciate that this can be confusing. + - For example, you may find a value of 4095, which is the maximum of an unsigned integer 12 bit image, which may be the datatype mentioned in the image metadata, however ImageJ may represent this image as a 16 bit image. Appreciate that this can be confusing! + - If you find the maximum of the image to be identical to to maximum that the datatype of the image can represent you may have an issue with saturation! Check this + - by hovering with the mouse over bright regions + - using the `HiLo` LUT with appropriate contrast settings, i.e. the maximum should be the maximum of your datatype! diff --git a/_includes/image_inspection_and_presentation/inspect_collagen_data.md b/_includes/image_inspection_and_presentation/inspect_collagen_data.md index e6e006e3..8c8ede9b 100644 --- a/_includes/image_inspection_and_presentation/inspect_collagen_data.md +++ b/_includes/image_inspection_and_presentation/inspect_collagen_data.md @@ -8,11 +8,10 @@ mentioned in this module's prerequisites. If you are a beginner, we recommend first learning the individual steps - [Inspect the image pixel values](https://neubias.github.io/training-resources/pixels/index.html#inspect_collagen) - [Adjust the image display](https://neubias.github.io/training-resources/lut/index.html#configure_luts) - - [Inspect image metadata and datatype](https://neubias.github.io/training-resources/datatypes/index.html#metadata_and_datatype) - - [Inspect microscope settings metadata](https://neubias.github.io/training-resources/image_file_formats/index.html#open) - - Of particular interest here is the image: Collagen - Molecular Devices TIFF with extensive metadata - - Find important metadata that affect the measurements, such as exposure time and illumination intensity - [Inspect and display spatial calibration](https://neubias.github.io/training-resources/spatial_calibration/index.html#scale_bar) + - [Inspect image data type](https://neubias.github.io/training-resources/datatypes/index.html#datatype_metadata) + - [Inspect microscope settings](https://neubias.github.io/training-resources/image_file_formats/index.html#open) + - Check out the collagen image and find important metadata, such as exposure time and illumination intensity ##### Image data diff --git a/_includes/pixels/collagen_inspection_imagejgui.md b/_includes/pixels/collagen_inspection_imagejgui.md index bf61c794..29546f61 100644 --- a/_includes/pixels/collagen_inspection_imagejgui.md +++ b/_includes/pixels/collagen_inspection_imagejgui.md @@ -5,5 +5,8 @@ - Mouse hover to see gray value and pixel position in the ImageJ status bar - Zoom in and out using the arrow up and down keys - Line profile: Draw a line ROI and use **[Analyze > Plot Profile]** or **[Ctrl + K]**. + - Use the ` Live ` button to explore different image regions - Histogram: **[Analyze > Histogram]** or **[Ctrl + H]** - - Optionally draw a rectangluar ROI to restrict the histogram computation to a small region containing bright collagen and background. + - Draw a rectangluar ROI to restrict the histogram computation to a small region + - Use the ` Live ` button to explore different image regions + - Understand what you see in the histogram