fixing docs

docs/index.rst

@@ -14,12 +14,14 @@ You can try it out without installing at `cellpose.org`_.
 Also check out these resources:
 
 Cellpose 2.0
+
 - `paper <https://youtu.be/3Y1VKcxjNy4>`_ on biorxiv
 - twitter `paper <https://youtu.be/3Y1VKcxjNy4>`_
 - human-in-the-loop training protocol `video <https://youtu.be/3Y1VKcxjNy4>`_
 
 Cellpose 1.0 
-- `paper`_ on biorxiv (see figure 1 below) and in `nature methods <>`_
+
+- `paper`_ on biorxiv (see figure 1 below) and in `nature methods <https://www.nature.com/articles/s41592-020-01018-x>`_
 - twitter `thread`_
 - Marius's `talk`_
 

docs/inputs.rst

@@ -19,8 +19,8 @@ nplanes x nY x nX. You can test this by running in python
 
 ::
 
-    import skimage.io
-    data = skimage.io.imread('img.tif')
+    import tifffile
+    data = tifffile.imread('img.tif')
     print(data.shape)
 
 If drag-and-drop of the tiff into 

docs/models.rst

@@ -23,8 +23,8 @@ starting from 4 different random initial parameter sets. This means you can
 run with ``diameter=0`` or ``--diameter 0`` and the model can estimate the ROI size. Also you can set 
 ``net_avg=True`` or ``--net_avg`` to average the results of the 4 models.
 
-These models can be loaded and used in the notebook with ``models.Cellpose(model_type='cyto')``
- or in the command line with ``python -m cellpose --pretrained_model cyto``.
+These models can be loaded and used in the notebook with ``models.Cellpose(model_type='cyto')`` 
+or in the command line with ``python -m cellpose --pretrained_model cyto``.
 
 Cytoplasm model (`'cyto'`)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^