Compressed-sensing imaging: towards low-phototoxicity and high-speed microscopy

Maxime Woringer*, under the supervision of Mustafa Mir, Christophe Zimmer and Xavier Darzacq.

Contact: maxime.woringer@ens.fr

Report & slides

cover

  • The report (version in progress, last updated 2016-09-06)
  • Slides (to be uploaded)

Contributed code

table

  1. http://github.com/pearu/pylibtiff/
  2. https://github.com/ricedsp/rwt
  3. http://drz.ac/code/spiraltap/
  4. https://gitlab.com/padouppadoup/SPIRAL-TAP
  5. https://gitlab.com/padouppadoup/pySPIRAL-TAP
  6. https://gitlab.com/padouppadoup/sparseNMF
  7. https://gitlab.com/padouppadoup/pyCSalgos

Glue code

This is mostly IPython notebook used to perform analysis. They can be found on the analysis notebooks archive. Note that this archive might not be up-to-date, but please email me if you are interested and I can share a git repository with the latest codes.

Movies

Some movies can be seen below.

Movies on simulations -- $\ell 1$-magic

All the movies show three stacked sequences, from left to right:

  1. Reconstructed image
  2. Original image
  3. Absolute error
In [2]:
from IPython.display import HTML

In space (over the $z$ positions)

In [3]:
HTML("""<video width="950" height="330" controls><source src="./vid/combined-space.webm"></video>""")
Out[3]:
In [4]:
HTML("""<video width="950" height="76" controls><source src="./vid/combined-space-reslice.webm"></video>""")
Out[4]:

In time (over 49 timepoints)

In [5]:
HTML("""<video width="950" height="330" controls><source src="./vid/combined-time.webm"></video>""")
Out[5]:
In [6]:
HTML("""<video width="950" height="50" controls><source src="./vid/combined-time-reslice.webm"></video>""")
Out[6]:

Movies acquired with the compressed sensing mode

Compressed version

In [14]:
HTML("""<center><video width="512" height="512" controls><source src="./vid/beads_compressed.webm"></video></center>""")
Out[14]:

Uncompressed version

Content of the sequences:

Original Reconstruction (full power)
Reconstruction (low power) Reconstruction (very low power)
In [12]:
HTML("""<video width="720" height="720" controls><source src="./vid/beads.webm"></video>""")
Out[12]:

Sources

The sources of the report, including high resolution figures are available.