Package: pygpseq
!DISCLAIMER!This package is not currently maintained. A new package that will include allpygpseqfeatures is being implemented atradiantkit.This package has been developed and tested ONLY for Python3.6, which will reach its end of life On December 23rd, 2021.Versions 3.4.* of this package only change package dependencies to fix an issue due to incorrect dependency declaration.pyGPSeqA Python3.6 package that provides tools to analyze images of GPSeq samples.
Read the Wikidocumentationfor more details.RequirementsPython3.6 and compatibletkinterpackage are required to runpygpseq.
On Ubuntu 20.04, you can install them with:sudoadd-apt-repositoryppa:deadsnakes/ppa
sudoaptinstallpython3.6
sudoaptinstallpython3.6-tkInstallationWe recommend installingpygpsequsingpoetry.
Check how to installpoetryhereif you don't have it yet! Once you havepoetryready on your system, you can install the
package in its own virtual environment with:gitclonehttps://github.com/ggirelli/pygpseq.gitcdpygpseq
poetryinstallAnd then enter the environment withpoetry shell.Alternatively, if you prefer to useconda, you can setup an environment with:condacreate-npygpseqpython=3.6
condaactivatepygpseq
condainstallpip
condainstall-canacondalibtiffUsageAnalyze a GPSeq image datasetThegpseq_anim(GPSeqanalysis ofimages) analyzes a multi-condition GPSeq image dataset. Rungpseq_anim -hfor more details.Calculate lamin distance of FISH signalsThegpseq_fromfishscript characterizes FISH signals identified withDOTTER(or similar tools) by calculating: absolute/normalized distance from lamina and central region, nuclear compartment, allele status,... Rungpseq_fromfish -hfor more details.Merge multiple FISH analyses using a metadata tableUse thegpseq_fromfish_mergescript to merge multiple FISH analysis output (generated withgpseq_fromfish). For more details rungpseq_fromfish_merge -h.Perform automatic 3D nuclei segmentationRuntiff_auto3dseg -hfor more details on how to produce binary/labeled (compressed) masks of your nuclei staining channelsIdentify out of focus (OOF) fields of viewRuntiff_findoof -hfor more details on how to quickly identify out of focus fields of view. Also, thetiff_plotoofscript (in R, requiresargparserandggplot2) can be used to produce an informative plot with the signal location over the Z stack.Split a tiff in smaller imagesTo split a large tiff to smaller square images of size N x N pixels, runtiff_split input_image output_folder N. Use the--enlargeoption to avoid pixel loss. If the input image is a 3D stack, then the output images will be of N x N x N voxels, use the--2dto apply the split only to the first slice of the stack. For more details, runtiff_split -h.(Un)compress a tiffTo uncompress a set of tiff, use thetiffcu -ucommand. To compress them use thetiffcu -ccommand instead. Usetiffcu -hfor more details.Convert a nd2 file into single-channel tiff imagesUse thend2_to_tifftool to convert images bundled into a nd2 file into separate single-channel tiff images. Usend2_to_tiff -hfor the documentation.ContributingWe welcome any contributions topygpseq. Please, refer to thecontribution guidelinesif this is your first time contributing! Also, check out ourcode of conduct.LicenseMIT License
Copyright (c) 2017-21 Gabriele Girelli