From 6b902e17fb90758ad1a826a82d772ced0a86a232 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Mon, 17 Mar 2025 17:39:25 -0500 Subject: [PATCH 1/4] Remove Definiens from list of software supporting OME-TIFF This software is no longer available, and no relevant websites are still online. --- ome-tiff/index.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/ome-tiff/index.rst b/ome-tiff/index.rst index 0d3513a..2ccb318 100644 --- a/ome-tiff/index.rst +++ b/ome-tiff/index.rst @@ -43,7 +43,6 @@ OME-TIFF is supported by: * `Bitplane AG `_ * `Carl Zeiss Microscopy GmbH `_ * `Cytiva `_ (formerly GE Healthcare, Applied Precision) -* `Definiens `_ * `DRVision Technologies LLC `_ * `Image-Pro by Media Cybernetics, Inc. `_ * `iMagic `_ From f4ec596cf08b499ce36007c2423b6568f58db709 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Mon, 17 Mar 2025 17:41:19 -0500 Subject: [PATCH 2/4] Remove excluded links that seem to be working now --- conf.py | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/conf.py b/conf.py index 55c1857..8426a69 100755 --- a/conf.py +++ b/conf.py @@ -324,19 +324,7 @@ 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 + "https://www.ncbi.nlm.nih.gov/pmc/.*" ] From 325b19b7d68be5691ea2bf1e1368ac9452cc63a3 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Tue, 18 Mar 2025 14:21:11 -0500 Subject: [PATCH 3/4] Update broken links --- ome-tiff/code.rst | 2 +- ome-tiff/data.rst | 2 +- ome-tiff/index.rst | 2 +- ome-tiff/specification.rst | 4 ++-- ome-tiff/tools.rst | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) 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 2ccb318..66b258d 100644 --- a/ome-tiff/index.rst +++ b/ome-tiff/index.rst @@ -41,7 +41,7 @@ OME-TIFF is supported by: * `BIOVIA `_ * `Bitplane AG `_ -* `Carl Zeiss Microscopy GmbH `_ +* `Carl Zeiss Microscopy GmbH `_ * `Cytiva `_ (formerly GE Healthcare, Applied Precision) * `DRVision Technologies LLC `_ * `Image-Pro by Media Cybernetics, Inc. `_ 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. From b810b19add14161a7dd7e9e8e8f0ec3524de7a99 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Tue, 18 Mar 2025 14:21:38 -0500 Subject: [PATCH 4/4] Update linkcheck excludes for things that work but fail build --- conf.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/conf.py b/conf.py index 8426a69..03dc2e1 100755 --- a/conf.py +++ b/conf.py @@ -326,5 +326,7 @@ def split_release(release): linkcheck_ignore = [ # 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://www.ncbi.nlm.nih.gov/pmc/.*", + "https://www.cytivalifesciences.com/", + "http://www.cellimagelibrary.org/" ]