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Pradeep Rajasekhar edited this page Dec 21, 2021 · 33 revisions

Gut Analysis Toolbox enables semi-automated analysis of the neurons and glia within the gut wall (enteric nervous system). It is a series of FIJI macros using StarDist and deepImageJ under the hood to do the heavy lifting with automated segmentation. The deep learning models supplied with GAT enable automated segmentation of:

  • enteric neuron soma (StarDist)
  • enteric neuronal subtypes (StarDist)
  • ganglia (deepImageJ)

The models have been trained using the easy to use notebooks from ZeroCostDL4Mic. The training data including the notebooks will be made available soon. The models will also be deposited on the BioImage Model Zoo.

Click on the sidebar to navigate through the WIKI.

Disclaimer: It is highly recommended to verify the output from the model and not to use it blindly. We have put a lot of effort into making sure the model works across a range of 2D images, but it is very likely that you may have to tune parameters by testing on your images. In some cases, you may need to train a new model.

You can also watch this as video tutorials on youtube by clicking on the image below.

GAT playlist

Over time, we will be introducing features such as multiplex registration and analysis, calcium imaging analysis and analysis of other cell types/image modalities related to gut research. Feel free to post an Issue.

Installation and configuration

Download FIJI from this link: https://imagej.net/software/fiji/downloads and unzip it on your computer.

  • To configure GAT, you will need to install a few plugins first

install_gat

  • You will get a pop up window that will check for updates:

install_gat

  • Once its done, the ImageJ Updater box will appear. Click Manage update sites on the bottom left and a window pops up:

install_gat

  • To install a plugin, tick on the corresponding boxes.

install_gat

Update sites

  • For installing GAT, tick on the following boxes:

    • BIG-EPFL
    • CSBDeep
    • clij
    • clij2
    • DeepImageJ
    • IJBP-Plugins (MorphoLibJ)
    • StarDist

  • You will also need to manually add the GAT update site. Click on “Add update site”

install_gat_update_site

  • A new row will appear with empty boxes under URL column.

install_gat_update_site

install_gat_update_site

  • Double click on “New” which is under the “Name” column and enter “GAT”.

install_gat_update_site

  • Hit Enter and then click “Close”.

  • All the dependencies and scripts from the update sites selected above will appear in the ImageJ Updater.

install_gat_update_site

  • Click “Apply changes” and once its finished, restart FIJI.

install_gat_update_site

install_gat_update_site

install_gat_update_site

Installing model files

  • Download the model zip file from this link.

  • Once downloaded, unzip the file and you will find a folder “models” within the unzipped folder.

gat_model

  • Move this “models” folder into your FIJI installation directory. In Windows and Mac it should be the FIJI.app folder.

gat_model

  • If you already had a models folder in there and asks if you’d like to replace files in the destination directory. Click “Yes”.

  • The models folder contains the 3 files required for running GAT:

    • Enteric neuron model: 2D_enteric_neuron_v4_1.zip
    • Enteric neuron subtype model: 2D_enteric_neuron_subtype_v4_1.zip
    • Ganglia model: 2D_enteric_ganglia_v2.bioimage.io.model

After all the installation and configuration, when you restart FIJI, you should see the GAT menu appear on FIJI.

gat_model

For a Mac, you can open the FIJI folder by right clicking on the folder:

gat_mac_model

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