microeye 2.3.5__tar.gz → 2.3.7__tar.gz

{microeye-2.3.5/src/microeye.egg-info → microeye-2.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.3.5
+Version: 2.3.7
 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
@@ -95,11 +95,11 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
 ```bash
- __  __ _            ___               ___   ____  ___ 
-|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ / | __|
-| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \_|__ \
-|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)___/
-                        |__/
+   __  ____              ____                ___    ____ ____
+  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  //_  /
+ / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ / / 
+/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)_/  
+                          /___/
 ```
 
 ## Table of Contents
@@ -121,6 +121,7 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
     - [Additional Hardware](#additional-hardware)
   - [Pycro-Manager Integration](#pycro-manager-integration)
     - [Features](#features)
+    - [Integrated Hardware](#integrated-hardware)
     - [How to Use](#how-to-use)
   - [Authors](#authors)
   - [People Involved](#people-involved)
@@ -317,25 +318,27 @@ Schematic overview of the miEye instrument:
 
 ### Supported Cameras
 
-| Camera                    | Description                                                  | Link                                                                                                  |
-| ------------------------- | ------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------- |
-| 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)                        |
-| Thorlabs DCC1545M         | DCx camera using UC480 driver                                | [Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                                  |
-| 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) |
+|          Camera           | Description                                                              |                                                     Link                                                      |
+| :-----------------------: | ------------------------------------------------------------------------ | :-----------------------------------------------------------------------------------------------------------: |
+| 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)             |
+|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
+| 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) |
+|    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)                |
+|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |                                                       -                                                       |
 
 ### Additional Hardware
 
 | Hardware                          | Description                                                                                                                                                           | Link                                                                                                                                                                                                   |
 | --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | [Link](https://integratedoptics.com/products/wavelength-combiners)                                                                                                                                     |
-| Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | [Link](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                                                                                                        |
+| Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | [Products Link](https://integratedoptics.com/products/wavelength-combiners)                                                                                                                            |
+| Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | [Piezo Concept FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                                                                                           |
 | 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) |
 | Thorlabs Elliptec ELL14           | Rotation Mount: SM1 Threaded                                                                                                                                          | [ELL14](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL14)                                                                                                                                     |
 | Thorlabs Elliptec ELL20           | Linear Stage: 60 mm Travel                                                                                                                                            | [ELL20](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL20)                                                                                                                                     |
-| 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)                                                                                                                                     |
-| Parallax TSL1401-DB (#28317)      | Linescan Camera Module                                                                                                                                                | [Link](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D)                                                                                     |
+| 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)                                                                                                                                   |
+| Parallax TSL1401-DB (#28317)      | Linescan Camera Module                                                                                                                                                | [Parallax TSL1401-DB](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D)                                                                      |
 | RelayBox Arduino                  | For laser control using camera GPIO signals                                                                                                                           | [RelayBox](https://github.com/samhitech/RelayBox)                                                                                                                                                      |
-| miEye OSF Project Parts List      | Parts list of miEye OSF Project                                                                                                                                       | [Link](https://osf.io/j2fqy/)                                                                                                                                                                          |
+| miEye OSF Project Parts List      | Parts list of miEye OSF Project                                                                                                                                       | [Repo Link](https://osf.io/j2fqy/)                                                                                                                                                                     |
 
 ## Pycro-Manager Integration
 
@@ -346,6 +349,15 @@ Integration with Pycro-Manager is now implemented, providing support for managin
 - **Headless Manager**: Manage multiple headless Micro-Manager instances (JavaBackend), including starting, stopping, and saving configurations.
 - **Core Instances Manager**: Handle multiple PycroCore instances for device communication and control.
 
+### Integrated Hardware
+
+The following table lists the hardware devices that are integrated and supported by the `miEye module`:
+
+| Device | Description                                                                                 |
+| :----: | ------------------------------------------------------------------------------------------- |
+| Camera | Access Micro-Manager cameras (mainly done for focus stabilization).                         |
+| ZStage | Access Micro-Manager Z-stage devices for focus stabilization and axial positioning control. |
+
 ### How to Use
 
 1. **Headless Manager**:
@@ -410,7 +422,7 @@ Special thanks to the following projects and libraries that make this work possi
   > 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)
 
 - **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:
-  > 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)
+  > 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)
 
 **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.
 

{microeye-2.3.5 → microeye-2.3.7}/README.md

@@ -31,11 +31,11 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
 ```bash
- __  __ _            ___               ___   ____  ___ 
-|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ / | __|
-| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \_|__ \
-|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)___/
-                        |__/
+   __  ____              ____                ___    ____ ____
+  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  //_  /
+ / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ / / 
+/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)_/  
+                          /___/
 ```
 
 ## Table of Contents
@@ -57,6 +57,7 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
     - [Additional Hardware](#additional-hardware)
   - [Pycro-Manager Integration](#pycro-manager-integration)
     - [Features](#features)
+    - [Integrated Hardware](#integrated-hardware)
     - [How to Use](#how-to-use)
   - [Authors](#authors)
   - [People Involved](#people-involved)
@@ -253,25 +254,27 @@ Schematic overview of the miEye instrument:
 
 ### Supported Cameras
 
-| Camera                    | Description                                                  | Link                                                                                                  |
-| ------------------------- | ------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------- |
-| 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)                        |
-| Thorlabs DCC1545M         | DCx camera using UC480 driver                                | [Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                                  |
-| 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) |
+|          Camera           | Description                                                              |                                                     Link                                                      |
+| :-----------------------: | ------------------------------------------------------------------------ | :-----------------------------------------------------------------------------------------------------------: |
+| 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)             |
+|     Thorlabs DCC1545M     | DCx camera using UC480 driver                                            |                 [Product Link](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M)                  |
+| 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) |
+|    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)                |
+|       Pycro-camera        | Access to cameras via Micro-Manager drivers/adapters using Pycro-Manager |                                                       -                                                       |
 
 ### Additional Hardware
 
 | Hardware                          | Description                                                                                                                                                           | Link                                                                                                                                                                                                   |
 | --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | [Link](https://integratedoptics.com/products/wavelength-combiners)                                                                                                                                     |
-| Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | [Link](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                                                                                                        |
+| Integrated Optics MatchBox        | Multi-wavelength Laser Combiner, Single Laser MatchBox                                                                                                                | [Products Link](https://integratedoptics.com/products/wavelength-combiners)                                                                                                                            |
+| Piezo Concept FOC                 | Nanopositioner for microscope objectives                                                                                                                              | [Piezo Concept FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc)                                                                                                                           |
 | 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) |
 | Thorlabs Elliptec ELL14           | Rotation Mount: SM1 Threaded                                                                                                                                          | [ELL14](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL14)                                                                                                                                     |
 | Thorlabs Elliptec ELL20           | Linear Stage: 60 mm Travel                                                                                                                                            | [ELL20](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL20)                                                                                                                                     |
-| 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)                                                                                                                                     |
-| Parallax TSL1401-DB (#28317)      | Linescan Camera Module                                                                                                                                                | [Link](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D)                                                                                     |
+| 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)                                                                                                                                   |
+| Parallax TSL1401-DB (#28317)      | Linescan Camera Module                                                                                                                                                | [Parallax TSL1401-DB](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D)                                                                      |
 | RelayBox Arduino                  | For laser control using camera GPIO signals                                                                                                                           | [RelayBox](https://github.com/samhitech/RelayBox)                                                                                                                                                      |
-| miEye OSF Project Parts List      | Parts list of miEye OSF Project                                                                                                                                       | [Link](https://osf.io/j2fqy/)                                                                                                                                                                          |
+| miEye OSF Project Parts List      | Parts list of miEye OSF Project                                                                                                                                       | [Repo Link](https://osf.io/j2fqy/)                                                                                                                                                                     |
 
 ## Pycro-Manager Integration
 
@@ -282,6 +285,15 @@ Integration with Pycro-Manager is now implemented, providing support for managin
 - **Headless Manager**: Manage multiple headless Micro-Manager instances (JavaBackend), including starting, stopping, and saving configurations.
 - **Core Instances Manager**: Handle multiple PycroCore instances for device communication and control.
 
+### Integrated Hardware
+
+The following table lists the hardware devices that are integrated and supported by the `miEye module`:
+
+| Device | Description                                                                                 |
+| :----: | ------------------------------------------------------------------------------------------- |
+| Camera | Access Micro-Manager cameras (mainly done for focus stabilization).                         |
+| ZStage | Access Micro-Manager Z-stage devices for focus stabilization and axial positioning control. |
+
 ### How to Use
 
 1. **Headless Manager**:
@@ -346,7 +358,7 @@ Special thanks to the following projects and libraries that make this work possi
   > 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)
 
 - **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:
-  > 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)
+  > 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)
 
 **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.
 

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/__init__.py

@@ -40,8 +40,3 @@ def getArgs():
 
 
 ARGS = getArgs()
-
-import microEye.analysis.fitting.pyfit3Dcspline as pyfit3Dcspline  # noqa: E402
-from microEye.analysis import multi_viewer  # noqa: E402
-from microEye.hardware import miEye_module  # noqa: E402
-from microEye.qt import *  # noqa: I001, E402

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 3, 5)
+version_info = (2, 3, 7)
 __version__ = '.'.join(map(str, version_info))

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/hardware/cams/camera_options.py

@@ -1,10 +1,9 @@
 import os
 import sys
 from enum import Enum
-from typing import Any, Optional
+from typing import Optional
 
 from pyqtgraph.parametertree import Parameter
-from pyqtgraph.parametertree.parameterTypes import GroupParameter
 
 from microEye.qt import QApplication, QtWidgets, Signal
 from microEye.utils.parameter_tree import Tree
@@ -729,7 +728,7 @@ class CameraOptions(Tree):
         str
             The selected dual view colors.
         '''
-        # get the selected dual view colors from the parameter tree e.g. 'RG', 'GB', etc.
+        # get the selected dual view colors from the parameter tree e.g. 'RG', 'GB', etc
         scheme = self.get_param_value(CamParams.DUAL_VIEW_COLORS)
 
         indices = {'R': 0, 'G': 1, 'B': 2}

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/hardware/cams/camera_panel.py

@@ -1,16 +1,11 @@
-import math
 import os
 import re
 import threading
-import time
 import traceback
-from functools import lru_cache
 from queue import Queue
-from typing import Optional, Union
+from typing import Union
 
-import cv2
 import numpy as np
-import pyqtgraph as pg
 
 from microEye.analysis.tools.roi_selectors import (
     MultiRectangularROISelector,
@@ -25,8 +20,7 @@ from microEye.hardware.cams.shortcuts import (
     CameraShortcutsWidget,
 )
 from microEye.qt import QDateTime, Qt, QtCore, QtWidgets, Signal, Slot
-from microEye.utils.display import DisplayManager
-from microEye.utils.expandable_groupbox import ExpandableGroupBox
+from microEye.utils.display import DisplayManager, fast_autolevels_opencv
 from microEye.utils.gui_helper import get_scaling_factor
 from microEye.utils.metadata_tree import MetadataEditorTree, MetaParams
 from microEye.utils.thread_worker import QThreadWorker
@@ -524,6 +518,21 @@ class Camera_Panel(QtWidgets.QGroupBox):
             except Exception:
                 traceback.print_exc()
 
+    def get_ROI(self) -> tuple[int, int, int, int]:
+        '''Gets the ROI for the selected camera.
+
+        Returns
+        -------
+        tuple[int, int, int, int]
+            The ROI as (x, y, width, height).
+        '''
+        x = self.camera_options.get_param_value(CamParams.ROI_X)
+        y = self.camera_options.get_param_value(CamParams.ROI_Y)
+        w = self.camera_options.get_param_value(CamParams.ROI_WIDTH)
+        h = self.camera_options.get_param_value(CamParams.ROI_HEIGHT)
+
+        return x, y, w, h
+
     def roi_shortcuts(self, fov: float, single: bool, software: bool):
         '''
         Sets the ROI for the camera using the selected FOV and mode.
@@ -560,6 +569,19 @@ class Camera_Panel(QtWidgets.QGroupBox):
             y = int((height - fov // pixel_size) / 2)
             h = int(fov // pixel_size)
 
+        if not software:
+            self.reset_ROI()
+            QtCore.QThread.msleep(250)  # wait for the camera to update the ROI
+
+            self.camera_options.set_param_value(CamParams.ROI_X, x)
+            self.camera_options.set_param_value(CamParams.ROI_Y, y)
+            self.camera_options.set_param_value(CamParams.ROI_WIDTH, w)
+            self.camera_options.set_param_value(CamParams.ROI_HEIGHT, h)
+
+            self.set_ROI()
+
+            x, y, w, h = self.get_ROI()
+
             rois = [
                 (x if software else 0, y if software else 0, h, h),
                 (h + 3 * x if software else h + 2 * x, y if software else 0, h, h),
@@ -576,18 +598,7 @@ class Camera_Panel(QtWidgets.QGroupBox):
                         'value': f'{roi[0]}, {roi[1]}, {roi[2]}, {roi[3]}',
                     },
                 )
-
-        if not software:
-            self.reset_ROI()
-            QtCore.QThread.msleep(250)  # wait for the camera to update the ROI
-
-            self.camera_options.set_param_value(CamParams.ROI_X, x)
-            self.camera_options.set_param_value(CamParams.ROI_Y, y)
-            self.camera_options.set_param_value(CamParams.ROI_WIDTH, w)
-            self.camera_options.set_param_value(CamParams.ROI_HEIGHT, h)
-
-            self.set_ROI()
-        elif single:
+        elif single and software:
             self.camera_options.add_param_child(
                 CamParams.EXPORTED_ROIS,
                 {
@@ -848,6 +859,10 @@ def display_frame(
     if isinstance(frame, uImage):
         frame = frame._image
 
+    thresholds, hist, cdf = fast_autolevels_opencv(
+        frame, levels=camp.camera_options.isAutostretch
+    )
+
     # cv2.imshow(name, frame)
     DisplayManager.instance().image_update_signal.emit(
         name,
@@ -862,6 +877,8 @@ def display_frame(
             'isROIsView': camp.camera_options.isROIsView,
             'isOverlaidView': camp.camera_options.isOverlaidView,
             'plot_type': camp.camera_options.isHistogramPlot,
+            'threshold': thresholds,
+            'plot': hist if camp.camera_options.isHistogramPlot else cdf,
         },
     )
 
@@ -890,7 +907,6 @@ def update_histogram_and_display(params: AcquisitionJob, camp: Camera_Panel):
         display_frame(camp, params.name, params.frame)
 
     elif camp.camera_options.isROIsView:
-
         overlaid = len(params.rois) == 2 and camp.camera_options.isOverlaidView
         flipped = camp.camera_options.isFlippedROIsView
 

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/hardware/cams/line_profiler.py

@@ -1,10 +1,9 @@
 import numpy as np
 import pyqtgraph as pg
 import qdarkstyle
-from pyqtgraph.multiprocess import proxy
 
 from microEye.analysis.tools.kymograms import get_kymogram_row
-from microEye.qt import QApplication, QtWidgets, Signal, Slot
+from microEye.qt import QApplication, QtWidgets, Signal
 
 
 class LineProfiler(QtWidgets.QWidget):

{microeye-2.3.5 → microeye-2.3.7}/src/microEye/hardware/cams/shortcuts.py

@@ -2,7 +2,7 @@ from typing import Union
 
 from microEye.hardware.cams.camera_options import CamParams
 from microEye.hardware.cams.micam import miCamera
-from microEye.qt import QDateTime, Qt, QtCore, QtGui, QtWidgets, Signal, Slot
+from microEye.qt import Qt, QtCore, QtGui, QtWidgets, Signal
 from microEye.utils.gui_helper import debounceSlot
 
 DEFAULT_EXPOSURE_SHORTCUTS = [
@@ -399,9 +399,7 @@ class CameraShortcutsWidget(QtWidgets.QWidget):
         # Close all windows
         self.close_windows_button = QtWidgets.QPushButton('Close All Windows')
         self.close_windows_button.setToolTip('Close all windows')
-        self.close_windows_button.clicked.connect(
-            lambda: self.closeAllWindows.emit()
-        )
+        self.close_windows_button.clicked.connect(lambda: self.closeAllWindows.emit())
         self.display_windows_btns.addWidget(self.close_windows_button)
 
     def _display_mode_changed(self, index):

microeye-2.3.7/src/microEye/hardware/cams/vimba/__init__.py

@@ -0,0 +1 @@
+

microeye-2.3.7/src/microEye/hardware/lasers/__init__.py

@@ -0,0 +1 @@
+