Crossbill project covers an open access single objective light-sheet microscopy platform. This repository covers the software aspect of this project. More details about this project is accessible at the accompanying bioRxiv pre-print at doi: 10.1101/2021.04.30.442190
An interactive 3D blender file for assembly and parts list is accessible at 10.5281/zenodo.6380689
OS dependence: Windows (this dependence is due to the DAQ and stage drivers used in the current project)
Install Instacal (from Measurement Computing) and MCL (MadCityLabs) drivers. This is not required for installation of crossbill, but is essential to successfully run the GUI.
Download this repository, unzip it and get to the /dist folder.
Run the following on the anaconda (https://www.anaconda.com/products/individual-d) commpand prompt.
Note: Admin previledges are required on this command prompt to be able to create required environment.
pip install crossbill-0.0.1-py3-none-any.whl (this .whl file is in the /dist folder)
Above is the most preferred approach, but alternate ones are listed below:
Download crossbill repository, unzip it, get to the folder containing setup.cfg file and then use the following:
conda create -n crossbill pip
conda activate crossbill
pip install -e . conda create -n crossbill python numpy pyqt qtpy qdarkstyle pip
conda activate crossbill
conda install -c conda-forge emoji
pip install mcculw Once installed, get to the crossbill-mini directory (download it from github or zenodo), and run crossbill-mini.py file with python:
cd crossbill-mini
python crossbill-mini.pyNote: src folder contents may be required to be manually copied to the crossbill-mini folder if 2nd approach for installation was used.
Some known errors:
- from crossbill.daq import MCCdaq (If an error shows up related to this line of code, it is likely due to missing Instacal - ensure that Instacal - from Measurement Computing - was installed properly.)
This contains 3D printable files related to the water chamber
This contains a python compatible GUI to provide software support for Crossbill microscope. This is windows compatible. Compatibility to other OS is limited due to incorporated hardware drivers.
This contains distribution files which may be used with the preferred pip install approach.
This contains an arduino compatible code which can be uploaded to a Raspberry Pi Pico board to be used with Crossbill microscope.
This folder has various functions/methods associated with DAQ and Stage.
Caution: This project (software) is in alpha phase of development!
MIT License
Copyright (c) 2021 Manish Kumar
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.