reads image data, spot locations, and surface locations from imaris files

filename = 'file.ims' x = ims_read(filename)

x.get_dataset_info()

for i in range(x.n_surf): x.get_surf_info(i)

for i in range(x.n_pts): x.get_pt_info(i)

x.save_image_data('filename', '.tif') # Each channel will be saved as filename_ch[0, 1, ...].tif

surf_n = 1 image_chan = x.surfs[surf_n]["ch"]

x.get_channel(image_chan) #(will be stored in x.data[n])

x.plot_surf_project(image_chan, surf_n, crop_area=None) # plot surface centers over a projection of an image channel, eg: x.plot_surf_project(image_chan, surf_n, crop_area=[750,1000,600,900])

Here, we are mostly reading in the surface centroids since we are interested in small objects, so this will not read out whole surface information (full surface shape)