diff --git a/Readme.md b/Readme.md index 2ef7586..6f061a2 100644 --- a/Readme.md +++ b/Readme.md @@ -2,9 +2,26 @@ ImageJ plugin for reading and writing HDF5 files. -For 3D datasets an individual slice can be selected for visualization. -Also, especially for very big datasets only every x-th slice can be selected -for visualization. This can be done by either specifying a number, e.g. `10` (for the slice 10) or a number with a preceding %, e.g. `%10` (for every 10th image). Indexing starts at 0. +Upon opening an HDF5 file, an import dialog lists the available image data sets +and allows the selection of one or multiple data sets to be opened: + +![Import dialog to select datasets to be opened](hdf5plugin_select_datasets.png) + +For 3D datasets, the whole data set is read into an image stack by default. +However, only individual slices can also be selected for visualization. +Furthermore, especially for very big datasets, only every n-th slice can be +selected for visualization. This can be done by either specifying a number, +e.g. `10` (for the slice 10) or a number with a preceding %, e.g. `%10` (for +every 10th image). Indexing starts at 0. Another useful feature when working +with lage data sets is the option to load the data into a virtual image stack. + +Note that the Fiji distribution of ImageJ comes with an hdf5 plugin already +installed out of the box. This packaged hdf5 plugin (HDF5_Vibez) has some great +features, and may be all you need. However, it does not allow one to load large +image arrays as virtual stacks, and thus often results in "out of memory" +errors when working with large data sets. In those cases, the PSI plugin for +reading and writing HDF5 files described here might be your preferred choice. + # Usage @@ -31,7 +48,51 @@ stack = reader.open("",False, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchang ``` # Installation -To be able to install this plugin ImageJ need to be run with a Java 7 or greater JVM. + +## Prerequisites +To be able to install this plugin, ImageJ need to be run with a Java 7 or +greater JVM. + +At the time of writing, the latest Fiji distribution of ImageJ comes bundled +with Java 8 by default, while older versions of ImageJ and Fiji are still using +Java 6. ImageJ itself (or more precisely the current ImageJ2 flavor of ImageJ) +seems to still be in a transitionary phase from Java 6 to Java 8 and does not +yet provide the full Java 8 functionality by default. The simplest option is +therefore to use a newer Fiji version which comes bundled with Java 8 for the +installation of this hdf5 plugin. + +The one caveat about using Fiji is that one needs to disable the pre-packaged +hdf5 plugin included in the distribution before installing this plugin. + +In the following, the installation procedure is detailed for a Fiji +installation with Java 8 included and also for older installations based on +Java 6. + +## Checking the Java version + +You can check whether Java-8 is included with Fiji as follows: + +* Open the update dialog from the menu via Fiji > Help > Update... +* Wait for the application to finish checking for new updates +* In the ImageJ Updater Window, click on "Advanced Mode" +* Type java-8 into the "Search" field. +* If you see an entry lib/Java-8 in the results box below, then Java 8 is ready + to be used on your system (see screenshots below). + + +## Download the source + +Download latest HDF5 ImageJ plugin from +[releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases). + + +## Installation for Fiji with Java 8 + + + + +## Installation for older versions of ImageJ/Fiji with Java 6 + * Download latest HDF5 ImageJ plugin from [releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases). diff --git a/hdf5plugin_select_datasets.png b/hdf5plugin_select_datasets.png new file mode 100644 index 0000000..1733b41 Binary files /dev/null and b/hdf5plugin_select_datasets.png differ