Cellpose test (win)

準備

Sample code

code:jupyter notebook

import numpy as np

import pandas as pd

from matplotlib import pyplot as plt

from cellpose import models, io, plot, core

from cellpose.io import imread

import torch

code:jupyter notebook

fname = 'Merge.tif'

imgs = io.imread(fname)

for img in imgs:

plt.figure(figsize=(2,2))

plt.imshow(img)

plt.axis('off')

plt.show()

code:jupyter notebook

use_GPU = core.use_gpu()

print('>>> GPU activated? %d'%use_GPU)

code:jupyter notebook

%%time

model = models.Cellpose(gpu=False, model_type="cyto3")

masks,flows = [],[]

for i,img in enumerate(imgs):

mask, flow, style, diam = model.eval(img, diameter=30,channels=chan)

masks.append(mask)

flows.append(flow)

io.save_to_png(img, mask, flow, 'mask/'+str(i)+'.png')

code:jupyter notebook

%%time

model = models.Cellpose(gpu=use_GPU, model_type='cyto3')

masks,flows = [],[]

for i,img in enumerate(imgs):

mask, flow, style, diam = model.eval(img, diameter=30,channels=chan)

masks.append(mask)

flows.append(flow)

io.save_to_png(img, mask, flow, 'mask/'+str(i)+'.png')

code:jupyter notebook

for img, mask,flow in zip(imgs,masks,flows):

fig = plt.figure(figsize=(12,5))

plt.tight_layout()

plt.show()

Apple Silicon Macの場合

Privateから転載

cellPose使い方

Web serverでの使い方

JPEGとかの画像をアップロードするだけ。お試し。

Jupyter notebookでの使い方

Anacondaが入っていたら、Prompt上で

pip install cellpose

G suite 共有ドライブ＞ Lab Protocol> Programming> jupyter notebook archivesにサンプルを入れています

Google colabでGPUを使ってみた。結構速い

Remarks

2024.07.01