import numpy as np import gradio as gr import spaces import cv2 from cellpose import models from matplotlib.colors import hsv_to_rgb import matplotlib.pyplot as plt import os, io, base64 from PIL import Image from cellpose.io import imread, imsave import glob from huggingface_hub import hf_hub_download img = np.zeros((96, 128), dtype = np.uint8) fp0 = Image.fromarray(img) #fp0 = "0.png" #imsave(fp0, img) # data retrieval def download_weights(): return hf_hub_download(repo_id="mouseland/cellpose-sam", filename="cpsam") #os.system("wget -q https://huggingface.co/mouseland/cellpose-sam/resolve/main/cpsam") def download_weights_old(): import os, requests fname = ['cpsam'] url = ["https://osf.io/d7c8e/download"] for j in range(len(url)): if not os.path.isfile(fname[j]): ntries = 0 while ntries<10: try: r = requests.get(url[j]) except: print("!!! Failed to download data !!!") ntries += 1 print(ntries) if r.status_code != requests.codes.ok: print("!!! Failed to download data !!!") else: with open(fname[j], "wb") as fid: fid.write(r.content) try: fpath = download_weights() model = models.CellposeModel(gpu=True, pretrained_model = fpath) except Exception as e: print(f"Error loading model: {e}") exit(1) def plot_flows(y): Y = (np.clip(normalize99(y[0][0]),0,1) - 0.5) * 2 X = (np.clip(normalize99(y[1][0]),0,1) - 0.5) * 2 H = (np.arctan2(Y, X) + np.pi) / (2*np.pi) S = normalize99(y[0][0]**2 + y[1][0]**2) HSV = np.concatenate((H[:,:,np.newaxis], S[:,:,np.newaxis], S[:,:,np.newaxis]), axis=-1) HSV = np.clip(HSV, 0.0, 1.0) flow = (hsv_to_rgb(HSV) * 255).astype(np.uint8) return flow def plot_outlines(img, masks): img = normalize99(img) img = np.clip(img, 0, 1) outpix = [] contours, hierarchy = cv2.findContours(masks.astype(np.int32), mode=cv2.RETR_FLOODFILL, method=cv2.CHAIN_APPROX_SIMPLE) for c in range(len(contours)): pix = contours[c].astype(int).squeeze() if len(pix)>4: peri = cv2.arcLength(contours[c], True) approx = cv2.approxPolyDP(contours[c], 0.001, True)[:,0,:] outpix.append(approx) figsize = (6,6) if img.shape[0]>img.shape[1]: figsize = (6*img.shape[1]/img.shape[0], 6) else: figsize = (6, 6*img.shape[0]/img.shape[1]) fig = plt.figure(figsize=figsize, facecolor='k') ax = fig.add_axes([0.0,0.0,1,1]) ax.set_xlim([0,img.shape[1]]) ax.set_ylim([0,img.shape[0]]) ax.imshow(img[::-1], origin='upper', aspect = 'auto') if outpix is not None: for o in outpix: ax.plot(o[:,0], img.shape[0]-o[:,1], color=[1,0,0], lw=1) ax.axis('off') #bytes_image = io.BytesIO() #plt.savefig(bytes_image, format='png', facecolor=fig.get_facecolor(), edgecolor='none') #bytes_image.seek(0) #img_arr = np.frombuffer(bytes_image.getvalue(), dtype=np.uint8) #bytes_image.close() #img = cv2.imdecode(img_arr, 1) #img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB) #del bytes_image #fig.clf() #plt.close(fig) buf = io.BytesIO() fig.savefig(buf, bbox_inches='tight') buf.seek(0) pil_img = Image.open(buf) plt.close(fig) return pil_img def plot_overlay(img, masks): if img.ndim>2: img_gray = img.astype(np.float32).mean(axis=-1) else: img_gray = img.astype(np.float32) img = normalize99(img_gray) #img = np.clip(img, 0, 1) HSV = np.zeros((img.shape[0], img.shape[1], 3), np.float32) HSV[:,:,2] = np.clip(img*1.5, 0, 1.0) for n in range(int(masks.max())): ipix = (masks==n+1).nonzero() HSV[ipix[0],ipix[1],0] = np.random.rand() HSV[ipix[0],ipix[1],1] = 1.0 RGB = (hsv_to_rgb(HSV) * 255).astype(np.uint8) return RGB def normalize99(img): X = img.copy() X = (X - np.percentile(X, 1)) / (1e-10 + np.percentile(X, 99) - np.percentile(X, 1)) return X def image_resize(img, resize=400): ny,nx = img.shape[:2] if np.array(img.shape).max() > resize: if ny>nx: nx = int(nx/ny * resize) ny = resize else: ny = int(ny/nx * resize) nx = resize shape = (nx,ny) img = cv2.resize(img, shape) img = img.astype(np.uint8) return img @spaces.GPU(duration=10) def run_model_gpu(img, max_iter): masks, flows, _ = model.eval(img, niter = max_iter)#, channels = [0,0]) return masks, flows @spaces.GPU(duration=60) def run_model_gpu60(img, max_iter): masks, flows, _ = model.eval(img, niter = max_iter)#, channels = [0,0]) return masks, flows @spaces.GPU(duration=240) def run_model_gpu240(img, max_iter): masks, flows, _ = model.eval(img, niter = max_iter)#, channels = [0,0]) return masks, flows import datetime from zipfile import ZipFile def cellpose_segment(filepath, resize = 1000,max_iter = 250): zip_path = os.path.splitext(filepath[-1])[0]+"_masks.zip" #zip_path = 'masks.zip' with ZipFile(zip_path, 'w') as myzip: for j in range((len(filepath))): now = datetime.datetime.now() formatted_now = now.strftime("%Y-%m-%d %H:%M:%S") img_input = imread(filepath[j]) #img_input = np.array(img_pil) img = image_resize(img_input, resize = resize) maxsize = np.max(img.shape) if maxsize<=1000: masks, flows = run_model_gpu(img, max_iter) elif maxsize < 5000: masks, flows = run_model_gpu60(img, max_iter) elif maxsize < 20000: masks, flows = run_model_gpu240(img, max_iter) else: raise ValueError("Image size must be less than 20,000") print(formatted_now, j, masks.max(), os.path.split(filepath[j])[-1]) target_size = (img_input.shape[1], img_input.shape[0]) if (target_size[0]!=img.shape[1] or target_size[1]!=img.shape[0]): # scale it back to keep the orignal size masks_rsz = cv2.resize(masks.astype('uint16'), target_size, interpolation=cv2.INTER_NEAREST).astype('uint16') else: masks_rsz = masks.copy() fname_masks = os.path.splitext(filepath[j])[0]+"_masks.tif" imsave(fname_masks, masks_rsz) myzip.write(fname_masks, arcname = os.path.split(fname_masks)[-1]) #masks, flows, _ = model.eval(img, channels=[0,0]) flows = flows[0] # masks = np.zeros(img.shape[:2]) # flows = np.zeros_like(img) outpix = plot_outlines(img, masks) #overlay = plot_overlay(img, masks) #crand = .2 + .8 * np.random.rand(np.max(masks.flatten()).astype('int')+1,).astype('float32') #crand[0] = 0 #overlay = Image.fromarray(overlay) flows = Image.fromarray(flows) Ly, Lx = img.shape[:2] outpix = outpix.resize((Lx, Ly), resample = Image.BICUBIC) #overlay = overlay.resize((Lx, Ly), resample = Image.BICUBIC) flows = flows.resize((Lx, Ly), resample = Image.BICUBIC) fname_out = os.path.splitext(filepath[-1])[0]+"_outlines.png" outpix.save(fname_out) #"outlines.png") #fname_flows = os.path.splitext(filepath[-1])[0]+"_flows.png" #flows.save(fname_flows) #"outlines.png") if len(filepath)>1: b1 = gr.DownloadButton(visible=True, value = zip_path) else: b1 = gr.DownloadButton(visible=True, value = fname_masks) b2 = gr.DownloadButton(visible=True, value = fname_out) #"outlines.png") return outpix, flows, b1, b2 def download_function(): b1 = gr.DownloadButton("Download masks as TIFF", visible=False) b2 = gr.DownloadButton("Download outline image as PNG", visible=False) return b1, b2 def tif_view(filepath): fpath, fext = os.path.splitext(filepath) if fext in ['tiff', 'tif']: img = imread(filepath[-1]) if img.ndim==2: img = np.tile(img[:,:,np.newxis], [1,1,3]) elif img.ndim==3: imin = np.argmin(img.shape) if imin<2: img = np.tranpose(img, [2, imin]) else: raise ValueError("TIF cannot have more than three dimensions") Ly, Lx, nchan = img.shape imgi = np.zeros((Ly, Lx, 3)) nn = np.minimum(3, img.shape[-1]) imgi[:,:,:nn] = img[:,:,:nn] #filepath = fpath+'.png' imsave(filepath, imgi) return filepath def norm_path(filepath): img = imread(filepath) img = normalize99(img) img = np.clip(img, 0, 1) fpath, fext = os.path.splitext(filepath) filepath = fpath +'.png' pil_image = Image.fromarray((255. * img).astype(np.uint8)) pil_image.save(filepath) #imsave(filepath, pil_image) return filepath def update_image(filepath): for f in filepath: f = tif_view(f) filepath_show = norm_path(filepath[-1]) return filepath_show, filepath, fp0, fp0 def update_button(filepath): filepath = tif_view(filepath) filepath_show = norm_path(filepath) return filepath_show, [filepath], fp0, fp0 with gr.Blocks(title = "Hello", css=".gradio-container {background:purple;}") as demo: #filepath = "" with gr.Row(): with gr.Column(scale=2): gr.HTML("""
Cellpose-SAM for cellular segmentation [paper] [github] [talk]
""") gr.HTML("""

You may need to login/refresh for 5 minutes of free GPU compute per day (enough to process hundreds of images).

""") input_image = gr.Image(label = "Input", type = "filepath") with gr.Row(): with gr.Column(scale=1): with gr.Row(): resize = gr.Number(label = 'max resize', value = 1000) max_iter = gr.Number(label = 'max iterations', value = 250) up_btn = gr.UploadButton("Multi-file upload (png, jpg, tif etc)", visible=True, file_count = "multiple") #gr.HTML("""

Note2: Only the first image of a tif will display the segmentations, but you can download segmentations for all planes.

""") with gr.Column(scale=1): send_btn = gr.Button("Run Cellpose-SAM") down_btn = gr.DownloadButton("Download masks (TIF)", visible=False) down_btn2 = gr.DownloadButton("Download outlines (PNG)", visible=False) with gr.Column(scale=2): outlines = gr.Image(label = "Outlines", type = "pil", format = 'png', value = fp0) #, width = "50vw", height = "20vw") #img_overlay = gr.Image(label = "Overlay", type = "pil", format = 'png') #, width = "50vw", height = "20vw") flows = gr.Image(label = "Cellpose flows", type = "pil", format = 'png', value = fp0) #, width = "50vw", height = "20vw") sample_list = glob.glob("samples/*.png") #sample_list = [] #for j in range(23): # sample_list.append("samples/img%0.2d.png"%j) gr.Examples(sample_list, fn = update_button, inputs=input_image, outputs = [input_image, up_btn, outlines, flows], examples_per_page=50, label = "Click on an example to try it") input_image.upload(update_button, input_image, [input_image, up_btn, outlines, flows]) up_btn.upload(update_image, up_btn, [input_image, up_btn, outlines, flows]) send_btn.click(cellpose_segment, [up_btn, resize, max_iter], [outlines, flows, down_btn, down_btn2]) #down_btn.click(download_function, None, [down_btn, down_btn2]) gr.HTML("""

Notes:
  • you can load and process 2D, multi-channel tifs.
  • the smallest dimension of a tif --> channels
  • you can upload multiple files and download a zip of the segmentations
  • install Cellpose-SAM locally for full functionality.

    • """) demo.launch()