microeye 2.4.4__tar.gz → 2.4.6__tar.gz

{microeye-2.4.4/src/microeye.egg-info → microeye-2.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.4.4
+Version: 2.4.6
 Summary: A python toolkit for fluorescence microscopy         that features hardware control, data analysis and vizualization         for super-resolution single-molecule localization microscopy and         single-partical tracking.
 Home-page: https://github.com/samhitech/microEye
 Author: Mohammad Nour Alsamsam
@@ -43,7 +43,7 @@ Requires-Dist: pyueye==4.96.952
 Requires-Dist: QDarkStyle==3.2.3
 Requires-Dist: QScintilla==2.14.1
 Requires-Dist: scikit-image==0.25.2
-Requires-Dist: scikit_learn==1.7.2
+Requires-Dist: scikit_learn==1.9.0
 Requires-Dist: scipy>=1.16.2
 Requires-Dist: setuptools>=80.9.0
 Requires-Dist: tables==3.10.2
@@ -65,20 +65,20 @@ Dynamic: summary
 
 # The microEye
 
-![microEye](https://github.com/samhitech/microEye/assets/89871015/37ca0859-0b4b-402d-8652-9a01d0bf0f29)
+<!-- ![microEye](https://github.com/samhitech/microEye/assets/89871015/37ca0859-0b4b-402d-8652-9a01d0bf0f29) -->
+
+```bash
+   __  ____              ____                ___  ____  ____
+  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / / / __/
+ / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _// _ \
+/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)_/(_)___/
+                          /___/
+```
 
 The **`microEye`** is a Python toolkit for fluorescence microscopy that supports super-resolution single-molecule localization microscopy and single-particle tracking. It features hardware control, data analysis, and visualization.
 
 This toolkit is compatible with the [hardware](#hardware) used in our microscope. For further details, refer to the [miEye microscope paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy).
 
-```bash
-   __  ____              ____                ___  ____ ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / // / /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _/_  _/
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)_/(_)_/  
-                          /___/   
-```
-
 <!-- ![Package Health](https://snyk.io/advisor/python/microEye/badge.svg) -->
 
 ![Python Version](https://img.shields.io/badge/Python-3.11-blue)
@@ -88,7 +88,8 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![Package Version](https://img.shields.io/badge/Windows-Tested-cyan)
 ![Package Version](https://img.shields.io/badge/MacOS-Errors-red)
 ![Package Version](https://img.shields.io/badge/Linux-NotTested-lightgray)
-![Downloads](https://img.shields.io/pypi/dm/microEye.svg)
+
+<!-- ![Downloads](https://img.shields.io/pypi/dm/microEye.svg) -->
 
 <!-- ![Dependencies](https://img.shields.io/librariesio/release/pypi/microEye) -->
 
@@ -160,6 +161,7 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
   Cameras from Basler, Allied Vision (Vimba X SDK), IDS Peak, Thorlabs,
   PCO, and PycroManager now share unified ROI, exposure, and framerate
   handling. Notable additions:
+  - **DCAM API v4 Support**: Full support for Hamamatsu sCMOS cameras via the DCAM API v4, tested with the ORCA-Fusion BT.
   - **IDS Peak** is newly supported with binning, flash, and full ROI and
     acquisition flow.
   - **Basler** is newly supported.
@@ -304,28 +306,28 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 >
 > _On Windows the `Vimba X installer` typically creates the `VIMBA_X_HOME` variable automatically — verify it before manually setting it._
 
-- Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
-- IDS CMOS cameras:
-  - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
-  - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
+- - Hamamatsu CMOS cameras: Install [`DCAM API v4`](https://www.hamamatsu.com/eu/en/product/cameras/software/driver-software/dcam-api-for-windows.html).
+  - Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
+  - IDS CMOS cameras:
+    - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
+    - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
 
 > [!TIP]
 >
 > - _The installation package also includes the uEye camera drivers for UI models in addition to the standard setup. Therefore, no installation of the IDS Software Suite is required for the operation of UI models._
 > - _If the process cannot read the system-wide `GENICAM_GENTL_PATH`/`GENICAM_GENTL64_PATH`, add the same variable to your User environment variables (not just System) and restart any open terminals or applications for the change to take effect._
 
-- Integrated Optics Lasers: Install [`Laser control software`](https://integratedoptics.com/downloads).
-
-- PCO cameras: Install [`pco.sdk`, `pco.runtime`](https://www.excelitas.com/product/pco-software-development-kits).
+- - Integrated Optics Lasers: Install [`Laser control software`](https://integratedoptics.com/downloads).
+  - PCO cameras: Install [`pco.sdk`, `pco.runtime`](https://www.excelitas.com/product/pco-software-development-kits).
 
 > [!NOTE]
 > **Support is under development.**
 
-- Thorlabs CMOS cameras: Install [`Thorcam`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory. Note: Some Thorlabs cameras may be identified as IDS uEye cameras by Windows and may run without Thorcam.
+- - Thorlabs CMOS cameras: Install [`Thorcam`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory. Note: Some Thorlabs cameras may be identified as IDS uEye cameras by Windows and may run without Thorcam.
 
-- Thorlabs hardware, install [`Kinesis® Software`](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [`Elliptec™ Software`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL).
+  - Thorlabs hardware, install [`Kinesis® Software`](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [`Elliptec™ Software`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL).
 
-4. **Open a terminal and execute microEye:** :partying_face:
+1. **Open a terminal and execute microEye:** :partying_face:
 
    ```powershell
    usage: microEye.exe [-h] [--module {mieye,viewer}] [--QT_API {PySide6,PyQt6,PyQt5}] [--theme {None,qdarktheme,qdarkstyle,...}]
@@ -478,13 +480,16 @@ Schematic overview of the miEye instrument:
 
 ### Supported Cameras
 
-|          Camera           | Description                                                              |             Driver             |                                                     Link                                                      |
-| :-----------------------: | ------------------------------------------------------------------------ | :----------------------------: | :-----------------------------------------------------------------------------------------------------------: |
-| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras                                        | `IDS uEye SDK 4.96.1` `pyueye` |            [Product Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html)             |
-|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |        `ThorCam 3.7.0`         |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
-| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m)             |     `Vimba X SDK` `vmbpy`      | [Product Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
-|    Excelitas PCO sCMOS    | Excelitas pco.edge 4.2 LT USB sCMOS Camera                               |     `pco.sdk` `pco.python`     |               [Product Link](https://www.excelitas.com/product/pcoedge-42-lt-usb-scmos-camera)                |
-|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |   `uManager` `Pycro-Manager`   |                                                       -                                                       |
+|          Camera           | Description                                                              |                  Driver                   |                                                     Link                                                      |
+| :-----------------------: | ------------------------------------------------------------------------ | :---------------------------------------: | :-----------------------------------------------------------------------------------------------------------: |
+|      Hamamatsu sCMOS      | Hamamatsu sCMOS cameras (e.g., ORCA-Flash4.0 V3, ORCA-Fusion BT)         |               `DCAM API v4`               |                 [Product Link](https://www.hamamatsu.com/eu/en/product/cameras/cmos-cameras/)                 |
+| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras                                        | `IDS uEye SDK 4.96.1` `IDS Peak` `pyueye` |            [Product Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html)             |
+|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |              `ThorCam 3.7.0`              |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
+| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m)             |           `Vimba X SDK` `vmbpy`           | [Product Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
+|    Basler ace 2 R PRO     | Basler `pylon` supported cameras                                         |             `pylon` `pypylon`             |                                                       -                                                       |
+|    Excelitas PCO sCMOS    | Excelitas pco.edge 4.2 LT USB sCMOS Camera                               |          `pco.sdk` `pco.python`           |               [Product Link](https://www.excelitas.com/product/pcoedge-42-lt-usb-scmos-camera)                |
+|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |        `uManager` `Pycro-Manager`         |                                                       -                                                       |
+
 
 ### Additional Hardware
 
@@ -492,6 +497,7 @@ Schematic overview of the miEye instrument:
 | --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
 | Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | `Native` |                                                              [Products Link](https://integratedoptics.com/products/wavelength-combiners)                                                               |
 | Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | `Native` |                                                              [Piezo Concept FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                              |
+| SmarAct MCS2                      | Support for SmarAct MCS2 multi-channel controllers                                                                                                                    | `Native` |                                                                                                   -                                                                                                    |
 | Thorlabs Elliptec ELL6/ELL9/ELL12 | Dual/Four/Six-Position Slider                                                                                                                                         | `Native` | [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) |
 | Thorlabs Elliptec ELL14           | Rotation Mount: SM1 Threaded                                                                                                                                          | `Native` |                                                                   [ELL14](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL14)                                                                   |
 | Thorlabs Elliptec ELL20           | Linear Stage: 60 mm Travel                                                                                                                                            | `Native` |                                                                   [ELL20](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL20)                                                                   |

{microeye-2.4.4 → microeye-2.4.6}/README.md

@@ -1,19 +1,19 @@
 # The microEye
 
-![microEye](https://github.com/samhitech/microEye/assets/89871015/37ca0859-0b4b-402d-8652-9a01d0bf0f29)
+<!-- ![microEye](https://github.com/samhitech/microEye/assets/89871015/37ca0859-0b4b-402d-8652-9a01d0bf0f29) -->
+
+```bash
+   __  ____              ____                ___  ____  ____
+  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / / / __/
+ / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _// _ \
+/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)_/(_)___/
+                          /___/
+```
 
 The **`microEye`** is a Python toolkit for fluorescence microscopy that supports super-resolution single-molecule localization microscopy and single-particle tracking. It features hardware control, data analysis, and visualization.
 
 This toolkit is compatible with the [hardware](#hardware) used in our microscope. For further details, refer to the [miEye microscope paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy).
 
-```bash
-   __  ____              ____                ___  ____ ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / // / /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _/_  _/
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)_/(_)_/  
-                          /___/   
-```
-
 <!-- ![Package Health](https://snyk.io/advisor/python/microEye/badge.svg) -->
 
 ![Python Version](https://img.shields.io/badge/Python-3.11-blue)
@@ -23,7 +23,8 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![Package Version](https://img.shields.io/badge/Windows-Tested-cyan)
 ![Package Version](https://img.shields.io/badge/MacOS-Errors-red)
 ![Package Version](https://img.shields.io/badge/Linux-NotTested-lightgray)
-![Downloads](https://img.shields.io/pypi/dm/microEye.svg)
+
+<!-- ![Downloads](https://img.shields.io/pypi/dm/microEye.svg) -->
 
 <!-- ![Dependencies](https://img.shields.io/librariesio/release/pypi/microEye) -->
 
@@ -95,6 +96,7 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
   Cameras from Basler, Allied Vision (Vimba X SDK), IDS Peak, Thorlabs,
   PCO, and PycroManager now share unified ROI, exposure, and framerate
   handling. Notable additions:
+  - **DCAM API v4 Support**: Full support for Hamamatsu sCMOS cameras via the DCAM API v4, tested with the ORCA-Fusion BT.
   - **IDS Peak** is newly supported with binning, flash, and full ROI and
     acquisition flow.
   - **Basler** is newly supported.
@@ -239,28 +241,28 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 >
 > _On Windows the `Vimba X installer` typically creates the `VIMBA_X_HOME` variable automatically — verify it before manually setting it._
 
-- Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
-- IDS CMOS cameras:
-  - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
-  - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
+- - Hamamatsu CMOS cameras: Install [`DCAM API v4`](https://www.hamamatsu.com/eu/en/product/cameras/software/driver-software/dcam-api-for-windows.html).
+  - Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
+  - IDS CMOS cameras:
+    - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
+    - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
 
 > [!TIP]
 >
 > - _The installation package also includes the uEye camera drivers for UI models in addition to the standard setup. Therefore, no installation of the IDS Software Suite is required for the operation of UI models._
 > - _If the process cannot read the system-wide `GENICAM_GENTL_PATH`/`GENICAM_GENTL64_PATH`, add the same variable to your User environment variables (not just System) and restart any open terminals or applications for the change to take effect._
 
-- Integrated Optics Lasers: Install [`Laser control software`](https://integratedoptics.com/downloads).
-
-- PCO cameras: Install [`pco.sdk`, `pco.runtime`](https://www.excelitas.com/product/pco-software-development-kits).
+- - Integrated Optics Lasers: Install [`Laser control software`](https://integratedoptics.com/downloads).
+  - PCO cameras: Install [`pco.sdk`, `pco.runtime`](https://www.excelitas.com/product/pco-software-development-kits).
 
 > [!NOTE]
 > **Support is under development.**
 
-- Thorlabs CMOS cameras: Install [`Thorcam`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory. Note: Some Thorlabs cameras may be identified as IDS uEye cameras by Windows and may run without Thorcam.
+- - Thorlabs CMOS cameras: Install [`Thorcam`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory. Note: Some Thorlabs cameras may be identified as IDS uEye cameras by Windows and may run without Thorcam.
 
-- Thorlabs hardware, install [`Kinesis® Software`](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [`Elliptec™ Software`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL).
+  - Thorlabs hardware, install [`Kinesis® Software`](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [`Elliptec™ Software`](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL).
 
-4. **Open a terminal and execute microEye:** :partying_face:
+1. **Open a terminal and execute microEye:** :partying_face:
 
    ```powershell
    usage: microEye.exe [-h] [--module {mieye,viewer}] [--QT_API {PySide6,PyQt6,PyQt5}] [--theme {None,qdarktheme,qdarkstyle,...}]
@@ -413,13 +415,16 @@ Schematic overview of the miEye instrument:
 
 ### Supported Cameras
 
-|          Camera           | Description                                                              |             Driver             |                                                     Link                                                      |
-| :-----------------------: | ------------------------------------------------------------------------ | :----------------------------: | :-----------------------------------------------------------------------------------------------------------: |
-| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras                                        | `IDS uEye SDK 4.96.1` `pyueye` |            [Product Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html)             |
-|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |        `ThorCam 3.7.0`         |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
-| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m)             |     `Vimba X SDK` `vmbpy`      | [Product Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
-|    Excelitas PCO sCMOS    | Excelitas pco.edge 4.2 LT USB sCMOS Camera                               |     `pco.sdk` `pco.python`     |               [Product Link](https://www.excelitas.com/product/pcoedge-42-lt-usb-scmos-camera)                |
-|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |   `uManager` `Pycro-Manager`   |                                                       -                                                       |
+|          Camera           | Description                                                              |                  Driver                   |                                                     Link                                                      |
+| :-----------------------: | ------------------------------------------------------------------------ | :---------------------------------------: | :-----------------------------------------------------------------------------------------------------------: |
+|      Hamamatsu sCMOS      | Hamamatsu sCMOS cameras (e.g., ORCA-Flash4.0 V3, ORCA-Fusion BT)         |               `DCAM API v4`               |                 [Product Link](https://www.hamamatsu.com/eu/en/product/cameras/cmos-cameras/)                 |
+| IDS uEye UI-3060CP Rev. 2 | IDS industrial-grade CMOS cameras                                        | `IDS uEye SDK 4.96.1` `IDS Peak` `pyueye` |            [Product Link](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html)             |
+|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |              `ThorCam 3.7.0`              |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
+| Allied Vision Alvium 1800 | Allied Vision industrial-grade CMOS cameras (U-158m, U-511m)             |           `Vimba X SDK` `vmbpy`           | [Product Link](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator) |
+|    Basler ace 2 R PRO     | Basler `pylon` supported cameras                                         |             `pylon` `pypylon`             |                                                       -                                                       |
+|    Excelitas PCO sCMOS    | Excelitas pco.edge 4.2 LT USB sCMOS Camera                               |          `pco.sdk` `pco.python`           |               [Product Link](https://www.excelitas.com/product/pcoedge-42-lt-usb-scmos-camera)                |
+|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |        `uManager` `Pycro-Manager`         |                                                       -                                                       |
+
 
 ### Additional Hardware
 
@@ -427,6 +432,7 @@ Schematic overview of the miEye instrument:
 | --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
 | Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | `Native` |                                                              [Products Link](https://integratedoptics.com/products/wavelength-combiners)                                                               |
 | Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | `Native` |                                                              [Piezo Concept FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                              |
+| SmarAct MCS2                      | Support for SmarAct MCS2 multi-channel controllers                                                                                                                    | `Native` |                                                                                                   -                                                                                                    |
 | Thorlabs Elliptec ELL6/ELL9/ELL12 | Dual/Four/Six-Position Slider                                                                                                                                         | `Native` | [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) |
 | Thorlabs Elliptec ELL14           | Rotation Mount: SM1 Threaded                                                                                                                                          | `Native` |                                                                   [ELL14](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL14)                                                                   |
 | Thorlabs Elliptec ELL20           | Linear Stage: 60 mm Travel                                                                                                                                            | `Native` |                                                                   [ELL20](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL20)                                                                   |

{microeye-2.4.4 → microeye-2.4.6}/src/microEye/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 4, 4)
+version_info = (2, 4, 6)
 __version__ = '.'.join(map(str, version_info))

{microeye-2.4.4 → microeye-2.4.6}/src/microEye/analysis/clustering/dbscan.py

@@ -4,7 +4,9 @@ from enum import Enum
 
 import numba as nb
 import numpy as np
-from sklearn.cluster import DBSCAN
+from hdbscan import HDBSCAN
+from scipy.spatial import ConvexHull, Delaunay, Voronoi
+from sklearn.cluster import DBSCAN, OPTICS, cluster_optics_dbscan
 from sklearn.preprocessing import StandardScaler
 
 logger = logging.getLogger(__name__)
@@ -417,11 +419,19 @@ def get_centers(
         return None
 
 
+def scale_data(x, y, z, sigma_xy=10.0, sigma_z=10.0):
+    if z is None:
+        return np.column_stack((x, y)), 1.0
+    else:
+        scale = sigma_xy / sigma_z
+        return np.column_stack((x, y, z * scale)), scale
+
+
 def perform_dbscan_clustering(X, Y, Z, eps=50, min_samples=2, **kwargs):
     '''
     Performs DBSCAN clustering on 3D localization data.
 
-    Parameters:
+    Parameters
     ------------
     X, Y, Z: array-like
         Arrays of x, y, z coordinates of localizations.
@@ -433,7 +443,10 @@ def perform_dbscan_clustering(X, Y, Z, eps=50, min_samples=2, **kwargs):
         a core point. Default is 2.
     **kwargs: additional keyword arguments for DBSCAN.
     '''
-    VECTORS = np.column_stack((X, Y, Z) if Z is not None else (X, Y))
+    sigma_xy = kwargs.pop('sigma_xy', 10.0)
+    sigma_z = kwargs.pop('sigma_z', 10.0)
+
+    VECTORS, scale = scale_data(X, Y, Z, sigma_xy, sigma_z)
 
     if kwargs.pop('scale_data', False):
         std = np.std(VECTORS)
@@ -443,13 +456,9 @@ def perform_dbscan_clustering(X, Y, Z, eps=50, min_samples=2, **kwargs):
         else:
             logger.warning('Standard deviation of data is zero. Skipping scaling.')
 
-    # 2. Initialize and fit DBSCAN
-    # eps: maximum distance between two samples
-    # min_samples: number of samples in a neighborhood for a point to be a core point
     dbscan_model = DBSCAN(eps=eps, min_samples=min_samples, **kwargs)
     dbscan_model.fit(VECTORS)
 
-    # 3. Retrieve labels (-1 indicates noise/outliers)
     labels = dbscan_model.labels_
     unique = np.unique(labels).shape[0] - 1
     logger.info(
@@ -457,3 +466,164 @@ def perform_dbscan_clustering(X, Y, Z, eps=50, min_samples=2, **kwargs):
     )  # Log only non-noise labels
 
     return labels
+
+
+def perform_hdbscan_clustering(X, Y, Z, **kwargs):
+    '''
+    Performs HDBSCAN clustering on 3D localization data.
+
+    Parameters
+    ------------
+    X, Y, Z: array-like
+        Arrays of x, y, z coordinates of localizations.
+    min_cluster_size: int, optional
+        The minimum size of clusters; single linkage splits that contain fewer
+        than this many samples are considered noise. Default is 5.
+    **kwargs: additional keyword arguments for HDBSCAN.
+    '''
+    sigma_xy = kwargs.pop('sigma_xy', 10.0)
+    sigma_z = kwargs.pop('sigma_z', 10.0)
+
+    VECTORS, scale = scale_data(X, Y, Z, sigma_xy, sigma_z)
+
+    if kwargs.pop('scale_data', False):
+        std = np.std(VECTORS)
+        if std > 0:
+            VECTORS /= std
+
+            kwargs['cluster_selection_epsilon'] = float(
+                kwargs.get('cluster_selection_epsilon', 0.0) / std
+            )
+            kwargs['cluster_selection_epsilon_max'] = float(
+                kwargs.get('cluster_selection_epsilon_max', 0.0) / std
+            )
+        else:
+            logger.warning('Standard deviation of data is zero. Skipping scaling.')
+
+    hdbscan_model = HDBSCAN(**kwargs)
+    hdbscan_model.fit(VECTORS)
+
+    labels = hdbscan_model.labels_
+    unique = np.unique(labels).shape[0] - 1
+    logger.info(
+        'Cluster labels: %d (%d Points)', unique, labels[labels != -1].shape[0]
+    )  # Log only non-noise labels
+
+    return labels
+
+
+def perform_optics_clustering(X, Y, Z, min_samples=10, xi=0.05, **kwargs):
+    '''
+    Performs OPTICS clustering on 3D localization data.
+
+    Parameters
+    -----------
+    X, Y, Z: array-like
+        Arrays of x, y, z coordinates of localizations.
+    min_samples: int, optional
+        The number of samples in a neighborhood for a point to be considered
+        a core point. Default is 10.
+    xi: float, optional
+        Steepness threshold (ξ) — smaller xi = more, finer-grained clusters.
+        Default is 0.05.
+    kwargs:
+        additional keyword arguments for OPTICS.
+
+        - scale_data: bool, optional
+            If True, scales the data to unit variance before clustering.
+        - sigma_xy: float, optional
+            Standard deviation for x and y coordinates (in nm). Default is 10.0.
+        - sigma_z: float, optional
+            Standard deviation for z coordinate (in nm). Default is 10.0.
+        - OPTICS parameters: any other parameters accepted by sklearn.cluster.OPTICS.
+
+    Returns
+    --------
+    labels: array of int
+        Per-point labels; -1 is noise, same convention as DBSCAN.
+    '''
+    sigma_xy = kwargs.pop('sigma_xy', 10.0)
+    sigma_z = kwargs.pop('sigma_z', 10.0)
+
+    VECTORS, scale = scale_data(X, Y, Z, sigma_xy, sigma_z)
+
+    if kwargs.pop('scale_data', False):
+        std = np.std(VECTORS)
+        if std > 0:
+            VECTORS /= std
+
+            kwargs['max_eps'] = kwargs.get('max_eps', np.inf) / std
+            kwargs['eps'] = (
+                kwargs.get('eps') / std if kwargs.get('eps') is not None else None
+            )
+        else:
+            logger.warning('Standard deviation of data is zero. Skipping scaling.')
+
+    optics = OPTICS(min_samples=min_samples, xi=xi, **kwargs)
+    optics.fit(VECTORS)
+
+    labels = optics.labels_
+    unique = np.unique(labels).shape[0] - 1
+    logger.info(
+        'Cluster labels: %d (%d Points)', unique, labels[labels != -1].shape[0]
+    )  # Log only non-noise labels
+
+    return labels
+
+
+def optics_then_dbscan_sweep(
+    X, Y, Z, min_samples=10, eps_values=(5, 10, 15, 20, 30, 50), **kwargs
+):
+    '''
+    Performs OPTICS clustering on 3D localization data, then sweeps through a range of
+    eps values for DBSCAN clustering on the reachability plot.
+
+    Parameters
+    -----------
+    X, Y, Z: array-like
+        Arrays of x, y, z coordinates of localizations.
+    min_samples: int, optional
+        The number of samples in a neighborhood for a point to be considered
+        a core point. Default is 10.
+    eps_values: iterable of float, optional
+        A list of eps values to sweep through for DBSCAN clustering.
+        Default is (5, 10, 15, 20, 30, 50).
+
+    Returns
+    --------
+    results: dict
+        A dictionary where keys are eps values and values are the corresponding
+        cluster labels from DBSCAN.
+    '''
+    sigma_xy = kwargs.pop('sigma_xy', 10.0)
+    sigma_z = kwargs.pop('sigma_z', 10.0)
+
+    VECTORS, scale = scale_data(X, Y, Z, sigma_xy, sigma_z)
+
+    std = 0.0
+
+    if kwargs.pop('scale_data', False):
+        std = np.std(VECTORS)
+        if std > 0:
+            VECTORS /= std
+        else:
+            logger.warning('Standard deviation of data is zero. Skipping scaling.')
+
+    optics = OPTICS(
+        min_samples=min_samples,
+        cluster_method=kwargs.pop('cluster_method', 'dbscan'),
+        **kwargs,
+    )
+    optics.fit(VECTORS)
+
+    results = {}
+    for eps in eps_values:
+        labels = cluster_optics_dbscan(
+            reachability=optics.reachability_,
+            core_distances=optics.core_distances_,
+            ordering=optics.ordering_,
+            eps=eps / std if std > 0 else eps,  # Scale eps if data was scaled
+        )
+        results[eps] = labels
+
+    return results