3D Image Analysis with qim3d
Felipe Delestro
fima@dtu.dk
QIM Center
Center for Quantification of Imaging Data from MAX IV
supported by
Rebecca
Engberg
Center Manager
Anders Bjorholm Dahl
Head of the QIM Center
Jon
Sporring
Deputy Head of the QIM Center
an open-source Python library, that focuses on 3D volumetric data
Getting started is easy:
pip install qim3d
Full documentation at https://platform.qim.dk/qim3d/
import qim3d
vol = qim3d.io.load("path/to/image.tif", virtual_stack=True)
Supported formats:
-
Tiff
(including file stacks) HDF5
-
TXRM
/TXM
/XRM
NIfTI
-
PIL
(including file stacks) -
VOL
/VGI
DICOM
qim3d.io.save("my_file.h5", vol)
import qim3d
vol = qim3d.examples.bone_128x128x128
blobs_256x256x256
bone_128x128x128
cement_128x128x128
fly_150x256x256
NT_128x128x128
shell_225x128x128
import qim3d
# Get data
vol = qim3d.examples.cement_128x128x128
vol_blurred = qim3d.processing.gaussian(vol, sigma=2)
# Detect blobs, and get binary mask
blobs, mask = qim3d.processing.blob_detection(
vol_blurred,
min_sigma=1,
max_sigma=8,
threshold=0.001,
overlap=0.1,
background="bright"
)
# Visualize detected blobs
qim3d.viz.circles(blobs, vol, alpha=0.8, color='blue')
import qim3d
vol = qim3d.examples.cement_128x128x128
binary = qim3d.processing.filters.gaussian(vol, 2)<60
qim3d.viz.slices(binary, axis=1)
labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
cmap = qim3d.viz.colormaps.objects(num_labels)
qim3d.viz.slices(labeled_volume, axis=1, cmap=cmap)
cmap = qim3d.viz.colormaps.objects(num_labels, style='bright', min_dist=0.5)
import qim3d
vol = qim3d.examples.cement_128x128x128[50:150]
vol_bin = vol<80
cc = qim3d.processing.get_3d_cc(vol_bin)
qim3d.viz.plot_cc(cc, crop=True, show=True, overlay=None, n_slices=5, component_indexs=[4])
qim3d.viz.plot_cc(cc, crop=True, show=True, overlay=vol, n_slices=5, component_indexs=[4])
import qim3d
vol = qim3d.examples.cement_128x128x128
qim3d.viz.slices(vol, vmin=0, vmax=255)
vol_filtered = qim3d.processing.operations.remove_background(vol,
min_object_radius=3,
background="bright")
qim3d.viz.slices(vol_filtered, vmin=0, vmax=255)
import qim3d
vol = qim3d.examples.cement_128x128x128
qim3d.viz.interactive_fade_mask(vol)
import qim3d
qim3d.viz.vol(vol)
import qim3d
vol_faded = qim3d.processing.operations.edge_fade(vol, decay_rate=4,
ratio=0.45,
geometric='cylindrical')
qim3d.viz.vol(vol_faded)
import qim3d
vol = qim3d.utils.generate_volume(noise_scale=0.05, threshold=0.4)
qim3d.viz.vol(vol)
import qim3d
vol = qim3d.examples.NT_128x128x128
val, vec = qim3d.processing.structure_tensor(vol, visualize=True, axis=2)
import qim3d
fly = qim3d.examples.fly_150x256x256
lt_fly = qim3d.processing.local_thickness(fly, visualize=True, axis=0)
qim3d gui --data-explorer
qim3d gui --local-thickness
Next steps of development
- Simplify dependencies
- Operations for large volumetric data (using
Dask
andZarr
) - Pre-trained DL models
- GUI for volumetric reconstruction (Using
CIL
) - GUI for volumetric data annotation
Author | Commits | First commit |
---|---|---|
Felipe Delestro | 170 | 2023-05-12 |
Stefan Engelmann Jensen | 29 | 2023-06-29 |
Oskar Kristoffersen | 15 | 2023-07-05 |
Christian Kento Rasmussen | 19 | 2024-02-01 |
Alessia Saccardo | 7 | 2024-02-19 |
David Grundfest | 4 | 2024-04-12 |
Anna Bøgevang Ekner | 3 | 2024-04-18 |
Thanks to all that contributed with code for qim3d
!
Find us at GitLab
lab.compute.dtu.dk/QIM/tools/qim3d
3D Image Analysis with qim3d
By Felipe Delestro
3D Image Analysis with qim3d
- 115