Cellpose CLI
See example usage at CLI examples. A description of the most important settings can be found on the Settings page.
Command Line Usage
Cellpose Command Line Parameters
usage: cellpose [-h] [--version] [--verbose] [--use_gpu]
[--gpu_device GPU_DEVICE] [--check_mkl] [--dir DIR]
[--image_path IMAGE_PATH] [--look_one_level_down]
[--img_filter IMG_FILTER] [--channel_axis CHANNEL_AXIS]
[--z_axis Z_AXIS] [--chan CHAN] [--chan2 CHAN2] [--invert]
[--all_channels] [--pretrained_model PRETRAINED_MODEL]
[--add_model ADD_MODEL] [--unet] [--nclasses NCLASSES]
[--no_resample] [--net_avg] [--no_interp] [--no_norm]
[--do_3D] [--diameter DIAMETER]
[--stitch_threshold STITCH_THRESHOLD] [--min_size MIN_SIZE]
[--fast_mode] [--flow_threshold FLOW_THRESHOLD]
[--cellprob_threshold CELLPROB_THRESHOLD]
[--anisotropy ANISOTROPY] [--exclude_on_edges] [--save_png]
[--save_tif] [--no_npy] [--savedir SAVEDIR] [--dir_above]
[--in_folders] [--save_flows] [--save_outlines] [--save_rois]
[--save_ncolor] [--save_txt] [--train] [--train_size]
[--test_dir TEST_DIR] [--mask_filter MASK_FILTER]
[--diam_mean DIAM_MEAN] [--learning_rate LEARNING_RATE]
[--weight_decay WEIGHT_DECAY] [--n_epochs N_EPOCHS]
[--batch_size BATCH_SIZE] [--min_train_masks MIN_TRAIN_MASKS]
[--residual_on RESIDUAL_ON] [--style_on STYLE_ON]
[--concatenation CONCATENATION] [--save_every SAVE_EVERY]
[--save_each]
Named Arguments
- --version
show cellpose version info
Default: False
- --verbose
show information about running and settings and save to log
Default: False
Hardware Arguments
- --use_gpu
use gpu if torch with cuda installed
Default: False
- --gpu_device
which gpu device to use, use an integer for torch, or mps for M1
Default: “0”
- --check_mkl
check if mkl working
Default: False
Input Image Arguments
- --dir
folder containing data to run or train on.
Default: []
- --image_path
if given and –dir not given, run on single image instead of folder (cannot train with this option)
Default: []
- --look_one_level_down
run processing on all subdirectories of current folder
Default: False
- --img_filter
end string for images to run on
Default: []
- --channel_axis
axis of image which corresponds to image channels
- --z_axis
axis of image which corresponds to Z dimension
- --chan
channel to segment; 0: GRAY, 1: RED, 2: GREEN, 3: BLUE. Default: 0
Default: 0
- --chan2
nuclear channel (if cyto, optional); 0: NONE, 1: RED, 2: GREEN, 3: BLUE. Default: 0
Default: 0
- --invert
invert grayscale channel
Default: False
- --all_channels
use all channels in image if using own model and images with special channels
Default: False
Model Arguments
- --pretrained_model
model to use for running or starting training
Default: “cyto”
- --add_model
model path to copy model to hidden .cellpose folder for using in GUI/CLI
- --unet
run standard unet instead of cellpose flow output
Default: False
- --nclasses
if running unet, choose 2 or 3; cellpose always uses 3
Default: 3
Algorithm Arguments
- --no_resample
disable dynamics on full image (makes algorithm faster for images with large diameters)
Default: False
- --net_avg
run 4 networks instead of 1 and average results
Default: False
- --no_interp
do not interpolate when running dynamics (was default)
Default: False
- --no_norm
do not normalize images (normalize=False)
Default: False
- --do_3D
process images as 3D stacks of images (nplanes x nchan x Ly x Lx
Default: False
- --diameter
cell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image
Default: 30.0
- --stitch_threshold
compute masks in 2D then stitch together masks with IoU>0.9 across planes
Default: 0.0
- --min_size
minimum number of pixels per mask, can turn off with -1
Default: 15
- --fast_mode
now equivalent to –no_resample; make code run faster by turning off resampling
Default: False
- --flow_threshold
flow error threshold, 0 turns off this optional QC step. Default: 0.4
Default: 0.4
- --cellprob_threshold
cellprob threshold, default is 0, decrease to find more and larger masks
Default: 0
- --anisotropy
anisotropy of volume in 3D
Default: 1.0
- --exclude_on_edges
discard masks which touch edges of image
Default: False
Output Arguments
- --save_png
save masks as png and outlines as text file for ImageJ
Default: False
- --save_tif
save masks as tif and outlines as text file for ImageJ
Default: False
- --no_npy
suppress saving of npy
Default: False
- --savedir
folder to which segmentation results will be saved (defaults to input image directory)
- --dir_above
save output folders adjacent to image folder instead of inside it (off by default)
Default: False
- --in_folders
flag to save output in folders (off by default)
Default: False
- --save_flows
whether or not to save RGB images of flows when masks are saved (disabled by default)
Default: False
- --save_outlines
whether or not to save RGB outline images when masks are saved (disabled by default)
Default: False
- --save_rois
whether or not to save ImageJ compatible ROI archive (disabled by default)
Default: False
- --save_ncolor
whether or not to save minimal “n-color” masks (disabled by default
Default: False
- --save_txt
flag to enable txt outlines for ImageJ (disabled by default)
Default: False
Training Arguments
- --train
train network using images in dir
Default: False
- --train_size
train size network at end of training
Default: False
- --test_dir
folder containing test data (optional)
Default: []
- --mask_filter
end string for masks to run on. use “_seg.npy” for manual annotations from the GUI. Default: “_masks”
Default: “_masks”
- --diam_mean
mean diameter to resize cells to during training – if starting from pretrained models it cannot be changed from 30.0
Default: 30.0
- --learning_rate
learning rate. Default: 0.2
Default: 0.2
- --weight_decay
weight decay. Default: 1e-05
Default: 1e-05
- --n_epochs
number of epochs. Default: 500
Default: 500
- --batch_size
batch size. Default: 8
Default: 8
- --min_train_masks
minimum number of masks a training image must have to be used. Default: 5
Default: 5
- --residual_on
use residual connections
Default: 1
- --style_on
use style vector
Default: 1
- --concatenation
concatenate downsampled layers with upsampled layers (off by default which means they are added)
Default: 0
- --save_every
number of epochs to skip between saves. Default: 100
Default: 100
- --save_each
save the model under a different filename per –save_every epoch for later comparsion
Default: False