A GPSeq image analysis package
A Python3 package that provides tools to analyze images of GPSeq samples.
- Read the GitHub pages documentation for more details.
- Read the Wiki documentation for more details.
Wiki docs will be merged with GitHub pages ones soon.
To install, run the following:
git clone http://github.com/ggirelli/pygpseq cd pygpseq sudo -H pip3 install .
To uninstall run the following from within the repository folder:
sudo -H pip3 uninstall pygpseq
To update, first uninstall, and then run the following from within the repository folder.
git pull sudo -H pip3 install .
Analyze a GPSeq image dataset
gpseq_anim (GPSeq analysis of images) analyzes a multi-condition GPSeq image dataset. Run
gpseq_anim -h for more details.
Calculate lamin distance of FISH signals
gpseq_fromfish script characterizes FISH signals identified with
DOTTER (or similar tools) by calculating: absolute/normalized distance from lamina and central region, nuclear compartment, allele status,... Run
gpseq_fromfish -h for more details.
Merge multiple FISH analyses using a metadata table
gpseq_fromfish_merge script to merge multiple FISH analysis output (generated with
gpseq_fromfish). For more details run
Perform automatic 3D nuclei segmentation
tiff_auto3dseg -h for more details on how to produce binary/labeled (compressed) masks of your nuclei staining channels
Identify out of focus (OOF) fields of view
tiff_findoof -h for more details on how to quickly identify out of focus fields of view. Also, the
tiff_plotoof script (in R, requires
ggplot2) can be used to produce an informative plot with the signal location over the Z stack.
Split a tiff in smaller images
To split a large tiff to smaller square images of size N x N pixels, run
tiff_split input_image output_folder N. Use the
--enlarge option 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
--2d to apply the split only to the first slice of the stack. For more details, run
(Un)compress a tiff
To uncompress a set of tiff, use the
tiffcu -u command. To compress them use the
tiffcu -c command instead. Use
tiffcu -h for more details.
Convert a nd2 file into single-channel tiff images
nd2_to_tiff tool to convert images bundled into a nd2 file into separate single-channel tiff images. Use
nd2_to_tiff -h for the documentation.
MIT License Copyright (c) 2017 Gabriele Girelli
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