Merge pull request #20 from jburel/fix_install

fix installation
ome · Jul 20, 2020 · ce7e39d · ce7e39d
2 parents 72f3fe1 + f3111f2
commit ce7e39d
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Showing 5 changed files with 33 additions and 4 deletions.
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -3,11 +3,32 @@ channels:
   - ome
   - ilastik-forge
 dependencies:
-  - omero-py
+  - omero-py  # ome
   - pip
-  - ilastik-dependencies-no-solvers==1.4
-  - ilastik-meta==1.4.0b5
+  # ilastik
+  - greenlet
+  - grpcio
+  - h5py
+  - tifffile
+  - scikit-image<=0.16
+  - scikit-learn
+  - yapsy
+  - vigra
+  - yapsy
+  - z5py
+  - elf==0.2.1.post7  # ilastik-forge
+  - fastfilters==0.2.6.post26  # ilastik-forge
+  - hytra==1.1.4.post66 # ilastik-forge
+  - ilastikrag==0.1.3.post38 # ilastik-forge
+  - ilastiktools==0.2.post32 # ilastik-forge
+  - ilastik-feature-selection  # ilastik-forge
+  - ilastik-meta==1.4.0b5  # ilastik-forge
+  - mamutexport==0.2.1.post5  # ilastik-forge
+  - ndstructs==0.0.1dev1  # ilastik-forge
+  - tiktorch==20.7.1  # ilastik-forge
+  # display
   - ipywidgets
+  # s3
   - zarr  # for scripts reading from S3
   - dask  # for scripts reading from S3
   - pip:

diff --git a/docs/gettingstarted.rst b/docs/gettingstarted.rst
@@ -7,7 +7,7 @@ Description
 We will use a Python script showing how to analyze data stored in an OMERO server
 using the ilastik API. The code snippets are extracted from the Python script
 :download:`pixel_classification.py <../scripts/pixel_classification.py>`. A notebook
-is also available, see `pixel_classification.ipynb <https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks>`_.
+is also available, see `idr0062_pixel_classification.ipynb <https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks/pixel_classification.ipynb>`_.
 
 
 We will show:

diff --git a/...books/pixel_classification_zarr_idr.ipynb → ...s/idr0062_pixel_classification_zarr.ipynb b/...books/pixel_classification_zarr_idr.ipynb → ...s/idr0062_pixel_classification_zarr.ipynb
diff --git a/notebooks/pixel_classification.ipynb b/notebooks/pixel_classification.ipynb
@@ -7,6 +7,10 @@
     "# Analyze data using ilastik\n",
     "The notebook shows how load images contained in a dataset\n",
     "from OMERO as numpy arrays and analyze them in ilastik.\n",
+    "The images are taken from  the paper \"NesSys: a novel method for accurate nuclear segmentation in 3D\" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388\n",
+    "\n",
+    "The images can be viewed online in the [Image Data Resource](https://idr.openmicroscopy.org/webclient/?show=project-801).\n",
+    "\n",
     "It assumes that ilastik project is linked to the dataset.\n",
     "The 5D-numpy array is in the order expected by the ilastik project.\n",
     "The order might need to be adjusted depending on the ilastik project."

diff --git a/notebooks/pixel_classification_zarr.ipynb b/notebooks/pixel_classification_zarr.ipynb
@@ -8,6 +8,10 @@
     "The notebook shows how load image contained in a dataset\n",
     "from OMERO and analyze them in ilastik.\n",
     "It assumes that ilastik project is linked to the dataset.\n",
+    "The images are taken from  the paper \"NesSys: a novel method for accurate nuclear segmentation in 3D\" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388\n",
+    "\n",
+    "The images can be viewed online in the [Image Data Resource](https://idr.openmicroscopy.org/webclient/?show=project-801).\n",
+    "\n",
     "The metadata are read from OMERO and the Binary data are read from S3.\n",
     "The ilastik results are saved as a zarr file and saved back to OMERO.\n",
     "The order might need to be adjusted depending on the ilastik project."