Merge pull request #732 from NEUBIAS/ome_zarr

Ome zarr

_includes/ome_zarr/ome_zarr_open_java_n5-ij-viewer.md

@@ -0,0 +1,81 @@
+<style>
+body {
+    font-size: 20px !important;
+}
+h3 {
+    font-size: 24px !important;
+}
+h4 {
+    font-size: 22px !important;
+}
+</style>
+
+### Open a remote OME-Zarr in Fiji
+- Open the n5-ij in Fiji via: 
+  - `[ File > Import > HDF5/N5/Zarr/OME-NGFF ... ]`<br><br>
+
+- In the window that opens, paste the following path in the uri space:
+  - `https://s3.embl.de/ome-zarr-course/data/commons/xyz_8bit_calibrated__fib_sem_crop.ome.zarr`<br><br>
+
+- Then click `Detect datasets` button as shown below: 
+<img src="{{ site.baseurl }}/figures/n5-ij/detect_datasets.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- The tool will display a multiscales schema with two datasets in the dialog box.
+Select one of the datasets as shown below and click OK:
+<img src="{{ site.baseurl }}/figures/n5-ij/select_dataset1.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- This will open the dataset in Fiji as a normal Fiji image (see below).
+<img src="{{ site.baseurl }}/figures/n5-ij/opened_dataset1.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+<h3>Open a subset of a remote OME-Zarr in Fiji</h3>
+- Follow the same steps above do select a dataset but instead of directly opening the dataset,
+click the crop button in the window before clicking OK as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-ij/select_dataset_and_crop2.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- In the window that open, select the indices of the subset as shown below: <br> 
+<img src="{{ site.baseurl }}/figures/n5-ij/select_dataset_and_crop1.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- When you click OK, the specified subset of the image will be opened as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-ij/cropped_dataset1.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+### Open a remote OME-Zarr in BigDataViewer
+
+Now let's imagine the dataset you want to open is too large to fit the RAM of your machine. 
+
+- Open the n5-viewer in Fiji via: 
+  - `[ Plugins > BigDataViewer > HDF5/N5/Zarr/OME-NGFF Viewer ]`<br><br>
+
+- In the window that opens, paste the following path in the uri space: 
+  - `https://s3.embl.de/i2k-2020/platy-raw.ome.zarr` <br><br>
+
+- Then click `Detect datasets` button as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-viewer/open_multiscales_detect.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- The tool will display a multiscales schema with 9 datasets in the dialog box.
+In this case, one can either open the individual datasets or the entire pyramid. 
+To do the latter, click on the multiscale object and then click OK as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-viewer/open_multiscales_object_effective.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- This will open the multiscales object in BDV as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-viewer/opened_multiscales.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- This is a huge (terabyte-scale) image, which is not amenable to processing as a whole
+in Fiji. It is possible, however, to extract subsets of it to Fiji and continue with processing. To do so, follow the steps below:<br><br>
+
+- In the BDV window, open the cropping window via: <br>
+`[ Tools > Extract to ImageJ ]` (also see below)
+
+<img src="{{ site.baseurl }}/figures/n5-viewer/extract_dataset.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+- In the cropping window that opens, select the indices of the subset as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-viewer/extract_dataset_ok.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br>
+Note that this step may require incremental rotation of the image and adjustment of the bounding box until
+the desired region of interest is obtained. It is also important to check the size of the cropped volume 
+at the top of the cropping window to make sure that it is not larger than the memory. Once you are fine
+with the settings, click OK.
+<br><br>
+- The output is a standard Fiji image as shown below: <br>
+<img src="{{ site.baseurl }}/figures/n5-viewer/extracted_image.png" alt="Detect Datasets" style="display: block; margin: 2px 0;" /><br><br>
+
+Note that this image has been loaded into the RAM; as such, it can be processed like any other 
+Fiji image and saved to any desired file format. 

_modules/ome_zarr.md

@@ -24,7 +24,7 @@ multiactivities:
   - ["ome_zarr/ome_zarr_inspection.md", [["minio-client", "ome_zarr/ome_zarr_inspection_minio-client.md"], ["ome-zarr-py","ome_zarr/ome_zarr_inspection_ome-zarr-py.md"]]]
   - ["ome_zarr/ome_zarr_performance.md", [["vizarr Chrome", "ome_zarr/ome_zarr_performance_vizarr_chrome.md"]]]
   - ["ome_zarr/ome_zarr_creation.md", [["BatchConvert", "ome_zarr/ome_zarr_creation_BatchConvert.md"]]]
-  - ["ome_zarr/ome_zarr_open_java.md", [["Fiji/MoBIE", "ome_zarr/ome_zarr_open_java_mobie.md"]]]
+  - ["ome_zarr/ome_zarr_open_java.md", [["Fiji/MoBIE", "ome_zarr/ome_zarr_open_java_mobie.md"], ["Fiji/n5-ij-viewer", "ome_zarr/ome_zarr_open_java_n5-ij-viewer.md"]]]
   - ["ome_zarr/ome_zarr_visualisation.md", [ ["napari","ome_zarr/ome_zarr_visualisation_napari.md"], ["Fiji/MoBIE", "ome_zarr/ome_zarr_visualisation_s3_mobie.md"], ["Neuroglancer","ome_zarr/ome_zarr_visualisation_s3_neuroglancer.md"], ["vizarr","ome_zarr/ome_zarr_visualisation_s3_vizarr.md"]]]
   - ["ome_zarr/ome_zarr_segmentation.md", [["ZarrSeg", "ome_zarr/ome_zarr_segmentation_zseg.md"]]]