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Bug fix
* Fixes `KeyError` bug produced during checking the convergence criteria by ordabayevy in

**Full Changelog**:


* cosmos model with Markov dependency by ordabayevy in

Bug fixes
* Fix nonspecific toggle bug by ordabayevy in
* Fix crosstalk model by ordabayevy in
* Bug fix. Remove `channels` option from the fit gui by ordabayevy in

**Full Changelog**:


* instead of specifying channel number to be analyzed now all color channels in the data are analyzed using multi-color cosmos models (see below)
* to analyze only a single color channel create a new folder and extract AOIs only for that particular color channel and then perform the analysis
* `channels-xxx` suffix was dropped from model and parameter files names
* model file and parameter file contents are not backward compatible

* cosmos model now supports multiple color channel analysis by ordabayevy in
* EXPERIMENTAL: multi-color cosmos model with crosstalk between channels by ordabayevy in

**Full Changelog**:


Breaking change
* New configuration file (`.tapqir/config.yaml`) is incompatible with previous versions of Tapqir

* Extend image distribution (KSMOGN) to support multi-dye multi-color data by ordabayevy in
* Add a GUI element for the offset histogram bin size by ordabayevy in
* Add GUI for prior inputs by ordabayevy in
* Add GUI for offset parameter inputs by ordabayevy in
* update docs to reflect new changes by ordabayevy in

* Fix ksmogn dist by ordabayevy in
* Lowercase Cosmos model name by ordabayevy in
* Move concatenation logic into handler by ordabayevy in
* Convert ndarray stats to list before saving summary by ordabayevy in

**Full Changelog**:


New features & GUI
* Field of View images are now also displayed in the Results GUI by ordabayevy in
* AOIs can be manually excluded from analysis by ordabayevy in
* Hide frame range instead of disabling by ordabayevy in

Internal & Fixes
* inputBox by ordabayevy in
* Update cosmos model reference by ordabayevy in
* Update docs by ordabayevy in

**Full Changelog**:


GUI & usability
* Make loading messages appear more responsive by ordabayevy in
* Reset offtarget path on toggle of `use offtarget` by ordabayevy in
* Validate paths in CLI application by ordabayevy in
* Handle errors and exceptions by ordabayevy in
* Add `View logs` tab by ordabayevy in
* Show summary table in results tab by ordabayevy in
* Disable load results button after the first click (reloading doesn't work) by ordabayevy in
* Update instructions accordingly by ordabayevy in

Bug fixes
* fix small bugs & clean up by ordabayevy in

Optimization & Internal
* Refactor SNR computation to avoid memory overflow by ordabayevy in
* Optimize `Cosmos.compute_probs` by ordabayevy in
* Add & use StatsMessenger to compute credible intervals by ordabayevy in
* Refactor load gui defaults by ordabayevy in
* Publish latest branch to TestPyPi by ordabayevy in
* Publish Python 🐍 distributions 📦 to PyPI by ordabayevy in
* Update python-app.yml by ordabayevy in

**Full Changelog**:


What's Changed
* Fix google colab installation by ordabayevy in
* Constrain to `click<=8.0.4` due to `ImporError` (

* Now to install Tapqir on desktop computers (Linux, WSL2) run `pip install tapqir[desktop]`

**Full Changelog**:


New changes
* Updated and significantly improved GUI
* Update to KeOps v2.0 in 295
* Pin to pyro-ppl==1.8.0 and torch==1.10.0 in 299
* Update and fix installation instructions
* Update README in 293
* Select offset bin size in 274
* Bug fixes


Initial Tapqir release

This version of the program was used to produce results in "Bayesian machine learning analysis of single-molecule fluorescence colocalization images" (Ordabayev et. al.).


- Single-color time-independent _cosmos_ model
- CLI (based on Typer) and GUI (based on Voila) interfaces
- Online Documentation and Tutorials



Has known vulnerabilities