cellpose
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MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
I successfully ran distributed segmentation of a 2D zarr array, but the code fails after processing all the chunks: ``` --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) Cell In[21], line...
When I try to segment using cellpose in Python I have an issue with setting the diameters. I provide the diameters in my script, but when I run the code...
Hi cellpose team, we are trying to use cellpose to segment high density, nuclear labeled, 3D data from zebrafish using a custom model. We use the stitching method to resolve...
**Describe the bug** I installed CellPose 3 on my computer and have been trying to get it to work. The cyto3 model works well for my images, though not perfect,...
**Describe the bug** I have been struggling with this for a few days. Please bear with me as I am not very good at coding yet and trying to fix...
**Describe the bug** Can't run a restore from CLI **To Reproduce** - fresh install cellpose 3.1.0 ``` mamba create -n cellpose-310 python=3.8 -y mamba activate cellpose-310 mamba install pytorch pytorch-cuda=11.8...
Resolve the following issues: Index error due to tensor dim mismatch and appears to minimize extra single pixel seeds often encountered in masks created with cellpose prior to 3.1.0 dynamics.py...
I created a new environment and did a fresh install. The red circle does disappear once I close the loop but it doesn't turn into a mask. I've drawn four...
@GFleishman, @carsen-stringer , @mrariden The purpose of this PR is to refactor the distributed_eval method so that I can use the code from this package directly in the command line...
use case: ``` import wandb from cellpose import models from pathlib import Path # Initialize experiment logging (e.g., W&B) wandb.init( project="cellpose-bacteria-segmentation", config={ "learning_rate": 0.0001, "epochs": 100, "batch_size": 8, "model_type": "cyto"...
