ucsdmanorlab / ims_reader

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

ims_reader

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

Usage:

initialize object

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

read in image info from the ims file (dimensions, number of channels, pixel size, ...)

x.get_dataset_info()

read surface area for all surfaces (or certain surfaces of interest):

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

read spot area for all spots objects (or certain spot objects of interest):

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

save out image data:

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

take note of which image channel was used to generate a surface:

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

pull image data from a specific channel

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

plot surface centers:

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])

Notes on functionality:

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)