PACMan

An chlorophyll-a fluorometry automation software designed for Walz (GMBH) Microscopy IPAM.

Confirmed to be compliant with V 2.51d of Imaging-Win Confirmed to be compliant with PRIOR ProScan III controller

PACKAGE REQUIREMENTS:

pyserial opencv comtypes ctypes numpy matplotlib skimage tkinter/ttk

REQUIREMENTS

• ImagingWin v2.51 (see Installing ImagingWin)
• Python 3.9
• Pip
• Windows 7/8/10

Installation of ImagingWin 2.51

• Windows 10: The remote control functionality is only enabled in specifically the v 2.51 exe version of the ImagingWin program. Due to this and ImagingWin supporting Windows 10 only on version >=2.56 the following steps must be taken to allow for remote control on Windows 10 systems: Install ImagingWin =2.56 as usual from Walz IMAGING-PAM download site (https://www.walz.com/products/chl_p700/imaging-pam_ms/downloads.html). After installation: Make copy of the ImagingWin.exe file located in the installation folder. Overwrite the ImagingWin.exe in the installation folder with the v 2.51 exe provided with PACMan.

Installation and use of PACMan

• Install correct version of ImagingWin as above
• Install with pip: pip install IPAM-PACMan

In your python IDE of choice:

• import pacman
• PacMan_instance = pacman.PacMan() This starts PacMan with the GUI turned on, in standard mode. To start PacMan in CLI mode:
• PacMan_instance = pacman.PacMan(False)

To start PacMan in Debug mode:

• PacMan_instance = pacman.PacMan(True/False,True)

To change PACsettings write pacman.open_settings()

Version history

v 1.0rc 19/03/2023

• Release Candidate
• Test installation performed
• Bug fixes

v 0.9.7 27/02/2023

• Technical Debt
  • Cleaning upp and testing installation file structure
  • Bug fixes
• Features
  • Added PACSettings.ini: A settings file to tell PACMan what features to use, pointing it to the local ImagingWin installation, default output dir etc.

v 0.9.5 25/01/2023

• Technical debt
  • Moved paths to ensure functionality after installation
• GUI fixes
  • Changed name of buttons to reflect functionality
• Documentation
  • Added error messages when PACMan cannot connect to stage

v 0.9.3 22/09/2022

• Created package

v 0.4.3 06/03/2022

• Started adding documentation for upload
• Cleaned up the github repository

v 0.4.2 06/12/2021

• About page added
• Cleaned up code slightly

v 0.4 15/11/2021 -Platform independent setup created -Execute acquistion moved into main class -Boilerplate code for stage communicator added

v 0.4 17/08/21

• Position list saving added into main
• Command queuing added
• More options for autofocus added
• Autofocus rescaled

v 0.3 3/07/2021

• Direct serial communication added
• Position list saving added (debug mode)

v 0.2.5 06/2022

• Tabs added to GUI. Main/Autofocus/position
• Position list added

v 0.2 05/2022 Autofocus implemented

v 0.1 04/2022 Basic functionality

Copyright (C) 2022 Olle Pontén

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/. Contact: olle.ponten@gmail.com