v0.7

What's Changed

• Updating User Dialogs by @mattyrowey in #18
• Added Dialog Boxes and Grammar Corrections by @mattyrowey in #19
• Updated Dialog Prompts for Clarity by @mattyrowey in #20
• Batch analysis option added.
• fixed a bunch of bugs related to ganglia segmentation and user workflow

New Contributors

• @mattyrowey made their first contribution in #18

Full Changelog: v0.6...v0.7

Custom ROI Imports

Added option for custom ROI imports for neurons and ganglia.
If neuronal or ganglia segmentation are done in separately, they can be imported into the workflow now.
To access this, 'tick' the "finetune detection parameters box" and this window appears:

To import the custom ROIs, tick the box on the right for the relevant marker.

For ganglia, select "import custom ROI" in the main window:

The files need to be Fiji ROI Managers. If you have a label image, you can convert them into ROIs by going to GAT -> Tools -> Commands -> Convert Label to ROIs

v0.5 Speed up and features!

• Speed up in workflows
  • ROI to label conversions and vice versa by using PT-BIOP update site
  • Morpholibj for generating label images instead of clij
• Option to collate all the results from analysis now added. Under "Analysis".
• Can specify different probability thresholds for neuronal subtypes now by using Finetune detections.
• New Documentation at: https://gut-analysis-toolbox.gitbook.io/docs/

v0.4 Fixed bugs with spatial analysis

• Fixed a few bugs with spatial analysis
• Simplified the GUI with checkboxes
• Spatial Analysis is now available as a checkbox through the main GUI for Neuronal and subtype neuronal analysis.

v0.3: Use rescaling factor instead of pixel size

For segmentation within FIJI, in earlier versions the user had to specify pixel size for rescaling which can be confused with the pixel size of the image.

As the aim is to rescale the image to a pixel size that gives accurate segmentation in StarDist, it is now renamed to rescaling factor.
Default is 1, which is equivalent to 0.568 micron/pixel -> Pixel size of the images used for training the StarDist models.
More information on conversions and calculations is in the documentation here.

Additional Video tutorial.

GAT - exciting changes!

Major changes:

• Ganglia segmentation using Hu only, Video link
• Multichannel neuron analysis without Hu labelling. Although, ganglia segmentation may have to be manual.
• Model files installed automatically when using GAT update sites. ImageJ updater now checks for files within models folder. 🥳

Minor changes:

• Added sample image and interactive 'clij' workflow for explaining theory for ganglia segmentation using Hu. Video for script
• Error Reporting options in GAT menu

v0.1

First release of Gut Analysis ToolBox with improved neuron modeld

zenodo link

Zenodo link now included
Better Docs