> For the complete documentation index, see [llms.txt](https://gut-analysis-toolbox.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://gut-analysis-toolbox.gitbook.io/docs/troubleshooting/list-of-major-bugs-fixed.md).

# List of major bugs fixed

This page is to document the issues we've encountered and fixed till date

This page is to track the bugfixes till date, and also for transparency. We are actively trying to fix bugs and keep GAT working!

**24/07/2025:** DeepImageJ bugs fixed. [#1](https://github.com/deepimagej/deepimagej-plugin/issues/59), [#2](https://github.com/deepimagej/deepimagej-plugin/issues/61), [#3](https://github.com/deepimagej/deepimagej-plugin/issues/64). StarDist plugin now used for neuron segmentation.

**24/05/2025:** DeepImageJ fixed, so all models including ganglia model works.

**23/05/2025:** Neuron segmentation models are fixed. Ganglia model is being[ looked into](https://github.com/bioimage-io/JDLL/issues/53).

**16/05/2025:** DeepImageJ error, where neuron and ganglia models are not being recognized. [More info here](https://github.com/deepimagej/deepimagej-plugin/issues/58).

**01/05/2025:** Updated ganglia model to v3 which uses pytorch. This works in deepImageJ.

**08/04/2025:** deepImageJ ganglia prediction is not working at the moment. Developer has been contacted.

**24/02/2025**: Ported the StarDist models to deepImageJ models for neuron prediction. This ensures GAT works, even if the StarDist plugin is not working. deepImageJ is used for all models, neuron, neuronal subtype and ganglia prediction. 

**10/02/2025:** The neuron prediction was not working. This was possibly due to updates in Fiji meaning that there were tensorflow configuration issues leading to StarDist plugin not working. Workarounds for getting Stardist running meant that deepImageJ did not work either. More info [here](https://forum.image.sc/t/stardist-plugin-error-after-fiji-update-only-custom-models/108026).

**10/02/2025**: The deepImageJ ganglia prediction was fixed.

**29/11/2024:** Updates to the deepImageJ plugin meant that the ganglia model would not work anymore. There were a few issues which meant it took longer to fix. More info [here](https://github.com/deepimagej/deepimagej-plugin/issues/52).


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