Merge pull request ome#179 from mtbc/LOCI-fixes

Various adjustments to follow LOCI site migration.

sphinx/about/index.rst

@@ -14,9 +14,9 @@ model <http://genomebiology.com/2005/6/5/R47>`_, particularly into the
 :model_doc:`OME-TIFF <ome-tiff>` file format.
 
 We believe the standardization of microscopy metadata to a common
-structure is of vital importance to the community. You may find LOCI's article
-on `open source software in
-science <https://loci.wisc.edu/software/oss>`_ of interest.
+structure is of vital importance to the community. You may find LOCI's
+article on `open source software in science
+<https://uw-loci.github.io/oss>`_ of interest.
 
 License, copyright, and citation
 --------------------------------
@@ -137,14 +137,14 @@ and C++ for many of its components (e.g., NumPy and SciPy), Java code is
 compiled one time into platform-independent byte code, which can be deployed
 as is to all supported platforms. And despite this enormous flexibility, Java
 manages to provide time performance nearly equal to C++, often better in the
-case of I/O operations (see further discussion on the
-`comparative speed of Java on the LOCI site <https://loci.wisc.edu/faq/isnt-java-too-slow>`_).
+case of I/O operations (see further discussion on the `comparative speed
+of Java on the LOCI site <https://uw-loci.github.io/why-java>`_).
 
 There are also historical reasons associated with the fact that the project
 grew out of work on the
 `VisAD Java component library <http://visad.ssec.wisc.edu>`_. You can read
 more about the origins of Bio-Formats on the
-`LOCI Bio-Formats homepage <https://loci.wisc.edu/software/bio-formats>`_.
+`LOCI Bio-Formats homepage <https://eliceirilab.org/software/bio-formats/>`_.
 
 Bio-Formats metadata processing
 -------------------------------

sphinx/developers/non-java-code.rst

@@ -8,9 +8,9 @@ in another language. But how to do so depends on your program's needs.
 Technologically, there are two broad categories of solutions:
 **in-process** approaches, and **inter-process** communication.
 
-For details, see LOCI's article
+For details, see LOCI's article,
 `Interfacing from non-Java code
-<http://loci.wisc.edu/software/interfacing-non-java-code>`_.
+<https://uw-loci.github.io/interfacing-non-java-code>`_.
 
 Example **in-process solution**: `Bio-Formats JACE C++ bindings <https://github.com/ome/bio-formats-jace>`_
 (note that this is a legacy project and no longer actively maintained).

sphinx/users/imagej/index.rst

@@ -23,7 +23,6 @@ The Bio-Formats Importer plugin can display image stacks in several
 ways:
 
 -  In a standard ImageJ window (including as a hyperstack)
--  Using the `LOCI Data Browser <http://loci.wisc.edu/software/data-browser>`_ plugin (included)
 -  With Joachim Walter's
    `Image5D <http://imagej.net/Image5D>`_ plugin
    (if installed)

sphinx/users/imagej/load-images.rst

@@ -76,10 +76,9 @@ Group files with similar names
 One of the most important features of Bio-Formats is to combine multiple
 files from a data set into one coherent, multi-dimensional image.
 
-To demonstrate how to use the **Group files with similar
-names** feature, you can use the `dub <http://loci.wisc.edu/sample-data/dub>`_
-data set available under LOCI’s `Sample
-Data <http://loci.wisc.edu/software/sample-data>`_ page. You will
+To demonstrate how to use the **Group files with similar names**
+feature, you can use the *dub* data set available under LOCI’s
+`Sample Data <https://scif.io/images/>`_ page. You will
 notice that it is a large dataset: each of the 85 files shows the
 specimen at 33 optical sections along the z-plane at a specific time.
 

sphinx/users/imagej/managing-memory.rst

@@ -11,7 +11,6 @@ warning like this:
 This means the allotted memory is less than what Bio-Formats needs to
 load all the images. If you have a very large data set, you may have to:
 
--  View your stack with Data Browser
 -  Crop the view area
 -  Open only a subset of images
 -  Use Virtual Stack
@@ -25,28 +24,6 @@ decompressed into memory before being displayed and require more memory
 than their file size suggests. If you are having this issue, try
 utilizing one of the memory management tools below.
 
-
-View your stack with Data Browser
----------------------------------
-
-**Data Browser** is another part of Bio-Formats that enables users to
-view large 3, 4, or 5-D datasets by caching a subset of all the images
-available. This enables users to view a stack that is bigger than the
-computer’s memory.
-
-You can select Data Browser as an option for **View stack with,** the
-leftmost, uppermost option in the **Bio-Formats Import Options** screen.
-
-.. image:: /images/DataBrowser.jpg
-   :align: center
-   :alt: Data Browser
-
-Note that when you use Data Browser, other features like cropping and
-specifying range are not available. You can, however, adjust the size
-of the image cache in the Data Browser after you open the files. You
-can read more about it on LOCI’s
-`Data Browser page <http://loci.wisc.edu/software/data-browser>`_.
-
 Cropping the view area
 ----------------------
 
@@ -69,8 +46,8 @@ Use Virtual Stack
 -----------------
 
 **Virtual Stack** conserves memory by not loading specific images until
-necessary. Note that unlike Data Browser, Virtual Stack does not contain
-a buffer and may produce choppy animations.
+necessary. Virtual Stack does not contain a buffer and may produce
+choppy animations.
 
 Increasing ImageJ/Fiji’s memory
 -------------------------------
@@ -85,7 +62,7 @@ ImageJ/Fiji by selecting **Memory & Threads** under the **Edit** menu.
 Generally, allocating more than 75% of the computer’s total memory will
 cause ImageJ/Fiji to become slow and unstable.
 
-**Please note** that unlike the other three features, ImageJ/Fiji itself
+**Please note** that, unlike the other two features, ImageJ/Fiji itself
 provides this feature and not Bio-Formats. You can find out more about
 this feature by looking at ImageJ’s
 `documentation <https://imagej.nih.gov/ij/docs/menus/edit.html#options>`_.

sphinx/users/visbio/index.rst

@@ -1,7 +1,7 @@
 VisBio
 ======
 
-`VisBio <http://loci.wisc.edu/software/visbio>`_ is a biological
+`VisBio <https://eliceirilab.org/visbio/>`_ is a biological
 visualization tool designed for easy visualization and analysis of
 multidimensional image data. VisBio uses Bio-Formats to import
 files as the Bio-Formats library originally grew out of our