Add workflow documentation for generic 2D EM workflow

docs/source/workflows/2d_EM.rst

@@ -0,0 +1,83 @@
+******
+Small 2D Workflow (EM Microscopy)
+******
+
+Overview:
+
+This workflow generates a thumbnail and a key images for each input image in a directory. Specific EM file formats
+use enhanced resampling and filtering techniques to reduce noise while adjusting the dynamic range of the images. This
+workflow originally was designed to handle DM3 files from TEM or STEM microscopes but has been extended to handle
+other 2D image file formats, including MRC, TIFF files and color figures.
+
+Outputs:
+ 1. A thumbnail image for each input image.
+   - An JPEG image with a maximum size of 300 pixels in both dimension.
+   - The aspect ratio is preserved and may be shortened to fit within the maximum size without padding.
+   - The image may be 8-bit RGB(A) or 8-bit gray-scale.
+ 2. A key image for each input image.
+   - Similar to the thumbnail image but with a maximum size of 1024 pixels in both dimension.
+
+.. list-table:: Supported Extensions for File Formats
+   :header-rows: 1
+
+   * - Format Type
+     - Description
+     - Extensions
+   * - DM3
+     - image format used by Digital Micrograph
+     - dm3
+   * - DM4
+     - image format used by Digital Micrograph, maybe limited to 64-bit integers
+     - dm4
+   * - MRC
+     - image format used by the IMOD tool suite
+     - mrc
+   * - TIFF
+     - Standard Tag Image File Format ( TIFF 6.0 ), OME TIFF not supported
+     - TIFF stacks not supported, only the first page is processed.
+     - tif, tiff
+   * - PNG
+     - Portable Network Graphics
+     - png
+   * - JPEG
+     - Joint Photographic Experts Group
+     - jpg, jpeg
+
+
+The toolbox of `IMOD`_ is used primarily to process the EM images, along with `SimpleITK`_ for additional image
+processing tasks.
+
+
+.. list-table:: Summary of Input Image Types
+   :header-rows: 1
+
+   * - Format Type
+     - Pixel Type
+     - Description
+     - Processing Information
+   * - JPEG, PNG, TIFF
+     - 8-bit RGB (palette) or RGBA
+     - Example images include figure, TEM grid image or other illustrative images rendered into a color image.
+     - Images should directly resized without intensity scaling or advanced filtering.
+   * - TIFF, PNG, JPEG
+     - 8-bit gray-scale
+     - Images may be rendered EM images with captions or annotations.
+     - Images should directly resized without intensity scaling or advanced filtering.
+   * - TIFF
+     - 16-bit (signed or unsigned) gray-scale
+     - EM images with a high dynamic range.
+     - Use IMOD's `newstack`_ tool to resample, filter, and scale intensities to 8-bit.
+   * - DM4 or DM3 Images
+     - 32-bit float (after MRC conversion)
+     - Minimally processed EM images with a high dynamic range.
+     - Convert to MRC via `dm2mrc`_ command to 32-bit float MRC files, then use newstack to resample, filter, and scale
+       intensities to 8-bit TIFF.
+   * - MRC (2D only)
+     - 32-bit float ( no other current sample inputs )
+     - Expected EM images with likely high dynamic range.
+     - Convert to 8-bit TIFF via `newstack`_ command to resample, filter, and scale intensities to 8-bit.
+
+.. _IMOD: https://bio3d.colorado.edu/imod/
+.. _dm2mrc: https://bio3d.colorado.edu/imod/doc/man/dm2mrc.html
+.. _newstack: https://bio3d.colorado.edu/doc/man/newstack.html
+.. _SimpleITK: https://simpleitk.readthedocs.io/

docs/source/workflows/index.rst

@@ -7,3 +7,5 @@ Workflows
 
 .. _ref-workflow-spatial-omics:
 .. include:: spatialomics.rst
+
+.. include:: 2d_EM.rst

em_workflows/dm_conversion/flow.py

@@ -115,9 +115,9 @@ def convert_em_to_tiff(file_path: FilePath) -> Path:
     Performs the conversion of EM images to tiff format, adjusting the dynamic range and reducing the size of the image.
 
     Three types of files are detected to need conversion:
-    - mrc files are converted to tiff using newstack
-    - 16-bit tiff files are converted to 8 bit tiff
-    - dm3/dm4 files are converted to mrc using dm2mrc, then to tiff using newstack
+      - mrc files are converted to tiff using newstack
+      - 16-bit tiff files are converted to 8-bit tiff
+      - dm3/dm4 files are converted to mrc using dm2mrc, then to tiff using newstack
 
     EM images are broadly characterized by a low signal-to-noise ratio and a high dynamic range, often with potential
      outliers. Using newstack with shrink and antialiasing kernels is required to reduce the noise to produce a