Merge pull request #1108 from GFleishman/main

Documented using masks and preprocessing_steps in distributed rst

Author: carsen-stringer

docs/distributed.rst

@@ -11,14 +11,30 @@ of the whole dataset.
 
 Built to run on workstations or clusters. Blocks can be run in parallel, in series, or both. 
 Compute resources (GPUs, CPUs, and RAM) can be arbitrarily partitioned for parallel computing.
-Currently workstations  and LSF clusters are supported. SLURM clusters are
+Currently workstations and LSF clusters are supported. SLURM clusters are
 an easy addition - if you need this to run on a SLURM cluster `please post a feature request issue
 to the github repository <https://github.com/MouseLand/cellpose/issues>`_ and tag @GFleishman.
 
-The input data format must be a zarr array. Some functions are provided in the module to help
-convert your data to a zarr array, but not all formats or situations are covered. These are
-good opportunities to submit pull requests. Currently, the module must be run via the Python API,
-but making it available in the GUI is another good PR or feature request.
+The input data format must be a `zarr array <https://zarr.readthedocs.io/en/stable/>`_.
+Some functions are provided in the module to help convert your data to a zarr array, but
+not all formats or situations are covered. These are good opportunities to submit pull requests.
+Currently, the module must be run via the Python API, but making it available in the GUI
+is another good PR or feature request.
+
+Many images contain large volumes of background - i.e. parts of the image that do not contain
+sample. It would be a waste of resources to try and segment in these areas. Distributed Cellpose can
+take a foreground mask and will only process blocks that contain foreground. The mask does not have
+to be the same sampling rate (resolution) as the input data. It is only assumed that the input data
+and mask have the same field of view. So you can give a huge image and a small mask as long as the
+physical length of the axes (number of voxels times the voxel size in physical units) is the same.
+
+Preprocessing (for example Gaussian smoothing) can sometimes improve Cellpose performance. But
+preprocessing big data can be inconvenient. Distributed Cellpose can take a list of
+preprocessing steps, which is a list of functions and their arguments, and it will run those
+functions on the blocks before running Cellpose. This distributes any preprocessing steps you
+like along with Cellpose itself. This can be used in very creative ways. For example,
+currently to perform multi-channel segmentation, you must use preprocessing_steps to provide
+the second channel. See the examples below to learn how to do multi-channel segmentation.
 
 All user facing functions in the module have verbose docstrings that explain inputs and outputs.
 You can access these docstrings like this:
@@ -121,6 +137,7 @@ Wrap a folder of tiff images/tiles into a single zarr array without duplicating
 
     # Note tiff filenames must indicate the position of each file in the overall tile grid
     from cellpose.contrib.distributed_segmentation import wrap_folder_of_tiffs
+
     reconstructed_virtual_zarr_array = wrap_folder_of_tiffs(
         filname_pattern='/path/to/folder/of/*.tiff',
         block_index_pattern=r'_(Z)(\d+)(Y)(\d+)(X)(\d+)',
@@ -163,3 +180,98 @@ Run distributed Cellpose on an LSF cluster with 128 GPUs (e.g. Janelia cluster):
         cluster_kwargs=cluster_kwargs,
     )
 
+
+Use preprocessing_steps and a mask:
+
+.. code-block:: python
+
+   from scipy.ndimage import gaussian_filter
+   from cellpose.contrib.distributed_segmentation import distributed_eval
+
+    # parameterize cellpose however you like
+    model_kwargs = {'gpu':True, 'model_type':'cyto3'}  # can also use 'pretrained_model'
+    eval_kwargs = {'diameter':30,
+                   'z_axis':0,
+                   'channels':[0,0],
+                   'do_3D':True,
+    }
+    
+    # define compute resources for local workstation
+    cluster_kwargs = {
+        'n_workers':1,    # if you only have 1 gpu, then 1 worker is the right choice
+        'ncpus':8,
+        'memory_limit':'64GB',
+        'threads_per_worker':1,
+    }
+
+    # create preprocessing_steps
+    # Note : for any pp step, the first parameter must be image and the last must be crop
+    #        you can have any number of other parameters in between them
+    def pp_step_one(image, sigma, crop):
+        return gaussian_filter(image, sigma)
+
+    # You can sneak other big datasets into the distribution through pp steps
+    # the crop parameter contains the slices you need to get the correct block
+    def pp_step_two(image, crop):
+        return image - background_channel_zarr[crop] # make sure the other dataset is also zarr
+
+    # finally, put all preprocessing steps together
+    preprocessing_steps = [(pp_step_one, {'sigma':2.0}), (pp_step_two, {}),]
+    
+    # run segmentation
+    # outputs:
+    #     segments: zarr array containing labels
+    #     boxes: list of bounding boxes around all labels (very useful for navigating big data)
+    segments, boxes = distributed_eval(
+        input_zarr=large_zarr_array,
+        blocksize=(256, 256, 256),
+        write_path='/where/zarr/array/containing/results/will/be/written.zarr',
+        preprocessing_steps=preprocessing_steps,
+        mask=mask,
+        model_kwargs=model_kwargs,
+        eval_kwargs=eval_kwargs,
+        cluster_kwargs=cluster_kwargs,
+    )
+
+
+Multi-channel segmentation using preprocessing_steps:
+
+.. code-block:: python
+
+   from cellpose.contrib.distributed_segmentation import distributed_eval
+
+    # parameterize cellpose however you like
+    model_kwargs = {'gpu':True, 'model_type':'cyto3'}  # can also use 'pretrained_model'
+    eval_kwargs = {'diameter':30,
+                   'z_axis':0,
+                   'channels':[2,1],  # two channels along first axis
+                   'do_3D':True,
+    }
+
+    # define compute resources for local workstation
+    cluster_kwargs = {
+        'n_workers':1,    # if you only have 1 gpu, then 1 worker is the right choice
+        'ncpus':8,
+        'memory_limit':'64GB',
+        'threads_per_worker':1,
+    }
+
+    # preprocessing step to stack second channel onto first
+    def stack_channels(image, crop):
+        return np.stack((image, second_channel_zarr[crop]), axis=1) # second channel is also a zarr array
+    preprocessing_steps = [(stack_channels, {}),]
+
+    # run segmentation
+    # outputs:
+    #     segments: zarr array containing labels
+    #     boxes: list of bounding boxes around all labels (very useful for navigating big data)
+    segments, boxes = distributed_eval(
+        input_zarr=large_zarr_array,
+        blocksize=(256, 256, 256),
+        write_path='/where/zarr/array/containing/results/will/be/written.zarr',
+        preprocessing_steps=preprocessing_steps,  # sneaky multi-channel segmentation
+        model_kwargs=model_kwargs,
+        eval_kwargs=eval_kwargs,
+        cluster_kwargs=cluster_kwargs,
+    )
+