Merge pull request #1416 from MouseLand/fix_run_dynamics_and_flow_docs

Fix run dynamics and flow docs

Author: carsen-stringer

cellpose/cli.py

@@ -110,7 +110,7 @@ def get_arg_parser():
         help="minimum number of pixels per mask, can turn off with -1")
     algorithm_args.add_argument(
         "--flow3D_smooth", required=False, default=0, type=float, nargs='+',
-        help="stddev of gaussian for smoothing of dP for dynamics in 3D, default of 0 means no smoothing. Pass a list of values to allow smoothing of the ZYX axes independently")
+        help="stddev of gaussian for smoothing of dP for dynamics in 3D, default of 0 means no smoothing. If you are seeing increased fragmentation along the Z axis, or ring-artifacts, you can specify increased smoothing in the z-axis by providing a list, e.g. `--flow3D_smooth 2 1 1`.  Pass a list of values to allow smoothing of the ZYX axes independently")
     algorithm_args.add_argument(
         "--flow_threshold", default=0.4, type=float, help=
         "flow error threshold, 0 turns off this optional QC step. Default: %(default)s")

cellpose/gui/gui.py

@@ -1867,7 +1867,7 @@ def compute_cprob(self):
                 self.logger.error("Flows don't exist, try running model again.")
                 return
 
-            maski = dynamics.compute_masks_and_clean(
+            maski = dynamics.resize_and_compute_masks(
                 dP=dP,
                 cellprob=cellprob,
                 niter=niter,

cellpose/models.py

@@ -187,7 +187,7 @@ def eval(self, x, batch_size=8, resample=True, channels=None, channel_axis=None,
             flow_threshold (float, optional): flow error threshold (all cells with errors below threshold are kept) (not used for 3D). Defaults to 0.4.
             cellprob_threshold (float, optional): all pixels with value above threshold kept for masks, decrease to find more and larger masks. Defaults to 0.0.
             do_3D (bool, optional): set to True to run 3D segmentation on 3D/4D image input. Defaults to False.
-            flow3D_smooth (int or float or list of (int or float), optional): if do_3D and flow3D_smooth>0, smooth flows with gaussian filter of this stddev. List smooths the ZYX axes independently and must be length 3. Defaults to 0.
+            flow3D_smooth (int or float or list of (int or float), optional): if do_3D and flow3D_smooth>0, smooth flows with gaussian filter of this stddev. If you are seeing increased fragmentation along the Z axis, or ring-artifacts, you can specify increased smoothing in the z-axis by providing a list, e.g. `flow3D_smooth = [2, 1, 1]`. List smooths the ZYX axes independently and must be length 3. Defaults to 0.
             anisotropy (float, optional): for 3D segmentation, optional rescaling factor (e.g. set to 2.0 if Z is sampled half as dense as X or Y). Defaults to None.
             stitch_threshold (float, optional): if stitch_threshold>0.0 and not do_3D, masks are stitched in 3D to return volume segmentation. Defaults to 0.0.
             min_size (int, optional): all ROIs below this size, in pixels, will be discarded. Defaults to 15.