Timelapse illumination correction method [MICCAI 2020]

[gwaybio]

Hi @tying84 and @Mirkazemi - Thanks for making BASIC available for python.

In your 2020 paper "Background and Illumination Correction for Time-Lapse Microscopy Data with Correlated Foreground" you introduce an improved method for illumination correction in timelapse imaging.

Is code for this updated method available in python? The paper states:

We will also develop our method into a user-friendly software tool that a large biological community can benefit from.

Can you point me to this resource? @roshankern and I are very interested in applying your method! Thank you in advance

[yfukai]

Hi, thank you @gwaygenomics for your interest! We, @Nicholas-Schaub, @tdmorello, @tying84, and I, are now trying to develop a new version in the dev branch. That segmentation-aware weighting and some improved implementation will also be provided there. Please be patient for one or two months until it gets completed!

[gwaybio]

Thanks @yfukai - we look forward to applying your implementation.

[tying84]

The BaSiC code is already in Python. The one with the segmentation mask will also be added in a few weeks.

Tingying

Gregory Way @.***> schrieb am Fr. 27. Mai 2022 um 18:50:

Hi @tying84 https://github.com/tying84 and @Mirkazemi https://github.com/Mirkazemi - Thanks for making this code available on python.

In your 2020 paper "Background and Illumination Correction for Time-Lapse Microscopy Data with Correlated Foreground" https://link.springer.com/chapter/10.1007/978-3-030-59722-1_17 you introduce an improved method for illumination correction in timelapse imaging.

Is this code available in python? The paper states:

We will also develop our method into a user-friendly software tool that a large biological community can benefit from.

Can you point me to this resource? @roshankern https://github.com/roshankern and I are very interested in applying your method! Thank you in advance

— Reply to this email directly, view it on GitHub https://github.com/peng-lab/BaSiCPy/issues/65, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACXOKOZY7KQEB73SGLQDPH3VMD4OJANCNFSM5XEXYB2Q . You are receiving this because you were mentioned.Message ID: @.***>

[yfukai]

Implemented in the beta released version! Please check out the fitting_weight parameter. @gwaybio https://basicpy.readthedocs.io/en/latest/api.html#basicpy.basicpy.BaSiC.fit

[gwaybio]

perfect! Thanks @yfukai - @jenna-tomkinson, @roshankern, and I are looking forward to testing this out!