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microEye v2.3.6
Enhancements: - Moved histogram equalization of acquired images from `PyQtGraphDisplay` image update slot into the camera display thread to reduce GUI freeze if any. - `io_combiner` and `io_single_laser`: - Replaced Qt-based serial communication with pyserial for laser controls, as pyserial is faster to implement and supports the `read_until` method in blocking mode. This change aims to address occasional GUI freezes when displaying acquired images while the serial communication queries laser readings/settings and updates the GUI periodically. The previous send command method was inefficient and introduced lag. - The ideal solution would be to use a separate thread for serial communication, but this is not currently implemented. Other Changes: - Added a user guide for the image analysis features in the Tiff Viewer module. BUG TO BE FIXED: Issue with focus stabilization on `PycroStage` using Java backend causes significant GUI freeze. (tested with FOC100) Future Updates: - Finalized Pycro-Manager Integration with XY-Stage and Focus Stabilization. - MacOS compatibility testing - 3D Localization fitting from Experimental PSF - Introduction of 2D/3D Single-Particle Tracking
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‎README.md‎

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![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
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```bash
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__ __ _ ___ ___ ____ ___
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| \/ (_)__ _ _ ___| __| _ ___ __ _|_ ) |__ / | __|
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| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \_|__ \
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|_| |_|_\__|_| \___/___\_, \___| \_//___(_)___(_)___/
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|__/
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__ ____ ____ ___ ____ ____
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/ |/ (_)__________ / __/_ _____ _ __|_ | |_ / / __/
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/ /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_/ _ \
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/_/ /_/_/\__/_/ \___/___/\_, /\__/ |___/____(_)____(_)___/
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/___/
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```
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## Table of Contents
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- [Additional Hardware](#additional-hardware)
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- [Pycro-Manager Integration](#pycro-manager-integration)
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- [Features](#features)
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- [Integrated Hardware](#integrated-hardware)
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- [How to Use](#how-to-use)
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- [Authors](#authors)
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- [People Involved](#people-involved)
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### Supported Cameras
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| Camera | Description | Link |
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| ------------------------- | ------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------- |
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| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras | [Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html) |
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| Thorlabs DCC1545M | DCx camera using UC480 driver | [Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M) |
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| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m) | [Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
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| Camera | Description | Link |
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| :-----------------------: | ------------------------------------------------------------------------ | :-----------------------------------------------------------------------------------------------------------: |
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| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras | [Product Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html) |
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| Thorlabs DCC1545M | DCx camera using UC480 driver | [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M) |
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| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m) | [Product Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
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| Excelitas PCO sCMOS | Excelitas pco.edge 4.2 LT USB sCMOS Camera | [Product Link](https://www.excelitas.com/product/pcoedge-42-lt-usb-scmos-camera) |
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| Pycro-camera | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager | - |
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### Additional Hardware
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| Hardware | Description | Link |
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| --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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| Integrated Optics MatchBox | Multi-wavelength Laser Combiner, Single Laser MatchBox | [Link](https://integratedoptics.com/products/wavelength-combiners) |
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| Piezo Concept FOC | Nanopositioner for microscope objectives | [Link](https://piezoconcept-store.squarespace.com/1-axis/p/foc) |
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| Integrated Optics MatchBox | Multi-wavelength Laser Combiner, Single Laser MatchBox | [Products Link](https://integratedoptics.com/products/wavelength-combiners) |
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| Piezo Concept FOC | Nanopositioner for microscope objectives | [Piezo Concept FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc) |
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| Thorlabs Elliptec ELL6/ELL9/ELL12 | Dual/Four/Six-Position Slider | [ELL6](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL6), [ELL9](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL9), [ELL12](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL12) |
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| Thorlabs Elliptec ELL14 | Rotation Mount: SM1 Threaded | [ELL14](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL14) |
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| Thorlabs Elliptec ELL20 | Linear Stage: 60 mm Travel | [ELL20](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL20) |
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| Thorlabs KDC101 | Kinesis Controller for Z825B/[Z925B](https://www.thorlabs.com/thorproduct.cfm?partnumber=Z925B) actuators (Activate USB VCP to access the COM port in device manager) | [Link](https://www.thorlabs.com/thorproduct.cfm?partnumber=KDC101) |
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| Parallax TSL1401-DB (#28317) | Linescan Camera Module | [Link](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D) |
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| Thorlabs KDC101 | Kinesis Controller for Z825B/[Z925B](https://www.thorlabs.com/thorproduct.cfm?partnumber=Z925B) actuators (Activate USB VCP to access the COM port in device manager) | [KDC101](https://www.thorlabs.com/thorproduct.cfm?partnumber=KDC101) |
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| Parallax TSL1401-DB (#28317) | Linescan Camera Module | [Parallax TSL1401-DB](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D) |
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| RelayBox Arduino | For laser control using camera GPIO signals | [RelayBox](https://github.com/samhitech/RelayBox) |
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| miEye OSF Project Parts List | Parts list of miEye OSF Project | [Link](https://osf.io/j2fqy/) |
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| miEye OSF Project Parts List | Parts list of miEye OSF Project | [Repo Link](https://osf.io/j2fqy/) |
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## Pycro-Manager Integration
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- **Headless Manager**: Manage multiple headless Micro-Manager instances (JavaBackend), including starting, stopping, and saving configurations.
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- **Core Instances Manager**: Handle multiple PycroCore instances for device communication and control.
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### Integrated Hardware
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The following table lists the hardware devices that are integrated and supported by the `miEye module`:
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| Device | Description |
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| :----: | ------------------------------------------------------------------------------------------- |
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| Camera | Access Micro-Manager cameras (mainly done for focus stabilization). |
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| ZStage | Access Micro-Manager Z-stage devices for focus stabilization and axial positioning control. |
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### How to Use
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1. **Headless Manager**:
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> Raw data to results: a hands-on introduction and overview of computational analysis for single-molecule localization microscopy", Martens et al., (2022), Frontiers in Bioinformatics. [Paper](https://www.frontiersin.org/articles/10.3389/fbinf.2021.817254)
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- **TARDIS (Temporal Analysis of Relative Distances)**: We have developed a partial Python implementation of TARDIS without fitting for now. For more information, refer to the [TARDIS software releases](https://github.com/kjamartens/TARDIS-public). The underlying algorithms and scientific details of TARDIS are detailed in the manuscript:
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> Martens et al., “Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking”, Nature Methods (2024). [Link](https://rdcu.be/dv1sr)
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> Martens et al., “Temporal analysis of relative distances (TARDIS) is a robust, parameter-free alternative to single-particle tracking”, Nature Methods (2024). [Article](https://rdcu.be/dv1sr)
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**Note**: I'm committed to maintaining an accurate acknowledgment list for our project. However, if I inadvertently miss acknowledging your work, please don't hesitate to reach out to us. I appreciate your understanding, and I'm doing my best to manage all acknowledgments amidst my other responsibilities.
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