diff --git a/conf.py b/conf.py index 55c1857..03dc2e1 100755 --- a/conf.py +++ b/conf.py @@ -324,19 +324,9 @@ def split_release(release): # Regular expressions that match URIs that should not be checked when doing a linkcheck build linkcheck_ignore = [ - "http://www.definiens.com", - "https://www.imagic.ch/", - "https://github.com/ome/", - "https://strandls.com", # SSL certificate verify failed # See https://www.ncbi.nlm.nih.gov/pmc/about/copyright/ # The PMC web site restricts access by the default Sphinx agent "https://www.ncbi.nlm.nih.gov/pmc/.*", - "https://eliceirilab.org/.*", # ConnectTimeoutError - "https://www.fei.com/.*", # SSL certificate expired - "http://www.perkinelmer.com/", # 500 Error - "http://mayachitra.com/", # SSL certificate expired "https://www.cytivalifesciences.com/", - "https://www.mediacy.com/", # https://www.digicert.com/ does not trust the issuer, but link is valid - "http://www.bitplane.com", # SSL certificate expired - "https://imaris.oxinst.com/.*", # SSL certificate expired + "http://www.cellimagelibrary.org/" ] diff --git a/ome-tiff/code.rst b/ome-tiff/code.rst index c138548..67604e9 100644 --- a/ome-tiff/code.rst +++ b/ome-tiff/code.rst @@ -65,7 +65,7 @@ with: .. seealso:: - `BigTIFF file format specification `__ + `BigTIFF file format specification `__ Modifying a TIFF comment ------------------------ diff --git a/ome-tiff/data.rst b/ome-tiff/data.rst index e0528f0..ad8256c 100644 --- a/ome-tiff/data.rst +++ b/ome-tiff/data.rst @@ -27,7 +27,7 @@ and imaging this sample data. The datasets were acquired on a multiphoton workstation (2.1 GHz Athlon XP 3200+ with 1GB of RAM) using -`WiscScan `_. All image +`WiscScan `_. All image planes were collected at 512 × 512 resolution in 8-bit grayscale, with an integration value of 2. diff --git a/ome-tiff/index.rst b/ome-tiff/index.rst index 0d3513a..66b258d 100644 --- a/ome-tiff/index.rst +++ b/ome-tiff/index.rst @@ -41,9 +41,8 @@ OME-TIFF is supported by: * `BIOVIA `_ * `Bitplane AG `_ -* `Carl Zeiss Microscopy GmbH `_ +* `Carl Zeiss Microscopy GmbH `_ * `Cytiva `_ (formerly GE Healthcare, Applied Precision) -* `Definiens `_ * `DRVision Technologies LLC `_ * `Image-Pro by Media Cybernetics, Inc. `_ * `iMagic `_ diff --git a/ome-tiff/specification.rst b/ome-tiff/specification.rst index c63cba2..14ac344 100644 --- a/ome-tiff/specification.rst +++ b/ome-tiff/specification.rst @@ -14,7 +14,7 @@ An OME-TIFF dataset consists of: - one or more files in standard TIFF_ format with the file extension ``.ome.tif`` or ``.ome.tiff`` or - `BigTIFF format `_ + `BigTIFF format `_ with one of these same file extensions or a BigTIFF-specific extension ``.ome.tf2``, ``.ome.tf8`` or ``.ome.btf`` - a string of OME-XML metadata embedded in the ImageDescription tag of the @@ -50,7 +50,7 @@ specification) shows the organization of a TIFF header along with the placement of the OME-XML metadata block. Note this is for the TIFF standard specification only; the header structure is slightly different for BigTIFF; see the `BigTIFF file format specification -`__. A TIFF file can +`__. A TIFF file can contain any number of IFDs, with each one specifying an image plane along with certain accompanying metadata such as pixel dimensions, physical dimensions, bit depth, color table, etc. One of the fields an IFD can diff --git a/ome-tiff/tools.rst b/ome-tiff/tools.rst index efc0832..e981c57 100644 --- a/ome-tiff/tools.rst +++ b/ome-tiff/tools.rst @@ -28,7 +28,7 @@ If you are looking for a solution in Java, there are several options. Bio-Formats can read OME-TIFF files, as well as convert from many third-party formats into OME-TIFF format—see the :doc:`example source code page ` for specific examples. Alternatively, the open -source `ImageJ `_ application reads +source `ImageJ `_ application reads multi-page TIFF files, storing the TIFF comment into the associated FileInfo object's "description" field.