pyGPSeq v2.1.2
=======================
A Python package that provides tools to analyze images of GPSeq samples.
Sample scripts are available showing the code for single/batch runs.
Read the [documentation](https://github.com/ggirelli/gpseq-img-py/wiki) for more details.
Installation
-------------
To **install**, run the following:
```
git clone http://github.com/ggirelli/gpseq-img-py
cd gpseq-img-py
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 .
```
Usage
----------
#### Analyze a GPSeq image dataset
The `gpseq_anim` (**GPSeq** **an**alysis of **im**ages) analyzes a multi-condition GPSeq image dataset. Run `gpseq_anim -h` for more details.
#### Calculate lamin distance of FISH signals
The `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
Use the `gpseq_fromfish_merge` script to merge multiple FISH analysis output (generated with `gpseq_fromfish`). For more details run `gpseq_fromfish_merge -h`.
#### Perform automatic 3D nuclei segmentation
Run `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
Run `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 `argparser` and `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 `tiff_split -h`.
#### (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
Use the `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.
License
---
```
MIT License
Copyright (c) 2017 Gabriele Girelli
```
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