Polo Version 0.2.0

Update overview: Post April 2023 users please read!

This updated version of Polo adds the most recent National High-Throughput Crystallization Center @ HWI cocktail formulations which rolled out in April of 2023.

Users of the National High-Throughput Crystallization Center who would also like to use Polo for image analysis and classification should be sure to use this version of the software as previous versions do not include the most up to date formulations and are likely to apply an incorrect screen version to your imaging data which is likely to result in the incorrect cocktail information being assigned to wells.

Therefore it is critical runs submitted to the screening center post April 2023 use Polo version 0.2.0 or greater for all image analysis.

Analysis of images pre-April 2023 will still function normally with any version of Polo.

If you would like to compare cocktail screening versions, all formulations are available as part of this repository in scr/data/cocktail_data

Program installation

Download the software version that is appropriate for your machine. Currently Windows 10 and 11, Ubuntu 22 LTS, and Mac (non Apple silicon) should be supported. Other operating systems will need to install the dependencies described in the environment.yml file and run src/Polo.py as a Python program.

• Windows 10 and 11 = PoloWindows0.2.0.exe
• Mac Ventura = PoloMac0.2.0.dmg
• Ubuntu 22 LTS = PoloUbuntu0.2.0

Windows users should be able to run Polo simply by downloading and running the .exe file. You will likely get a warning telling you Polo is an unrecognized program; allow it to run anyway to use the software.

Due to increased security measures on newer Mac operating systems, Mac users may have additional hurdles to overcome to get Polo running. First, download the .dmg file, open and drag to applications then attempt to run the Polo program. Answer yes to any permission type questions the OS gives you or Polo may fail to execute. If Polo is not recognized as an executable file you may have to mark the program as executable using the terminal. Apple has a guide on how to do use this at this link.

If you have issues installing on these operating systems please reach out to the crystallization center; htslab@hwi.buffalo.edu.

Getting starting with Polo

If you have successfully installed Polo and are a new user you can checkout written and video tutorials on the main features of the program at
this link

Other changes

• Updated cocktail_metadata to reflect new formulation start date
• Updated PyInstaller version to utilize Tensorflow hooks to hopefully make packaging into exes more reliable on all operating systems
• Included commercial codes when cocktail data is displayed to the user
• Minor bug fixes relating to exporting images of a selected classification as a PowerPoint presentation

Polo Version 0.1.1

Polo Version 0.1.1

Main Updates

• Added ability to select which images to include in PowerPoint exports manually
• Added citation information
• Reduced sig figs shown in table viewer and optimization viewer
• General bug fixes mainly to run importing

Installation Guide

Windows 10

Download the Windows installer and double click to run it. Windows will likely tell you Polo is an unrecognized program. To continue with the installation click More Info and then Run Anyway.

Mac OS >= High Sierra and Ubuntu >= 20.04.1 LTS x86_64

Download the Polo version for your OS and un-compress the file. You can then run the program by double clicking or with the command ./Polo.exe. Make sure you allow execution of Polo as a program.

If you run into any issues, more information can be found at the Polo website install guide page.

All versions of the program may take up to a minute to launch depending on your computer specs.

Test Data

If you do not have your own screening images you can download test images from the test data release page.

For More Information …

Visit the Polo documentation website for guides, video tutorials and troubleshooting help.

Or read the paper here!

Cite Polo

If you find Polo helpful please site

Holleman, E.T., Duguid, E., Keefe, L.J. & Bowman, S.E.J. (2021). J. Appl. Cryst. 54, https://doi.org/10.1107/S1600576721000108 

and

Bruno AE, Charbonneau P, Newman J, Snell EH, So DR, et al. (2018) Classification of crystallization outcomes using deep convolutional neural networks. PLOS ONE 13(6): e0198883. https://doi.org/10.1371/journal.pone.0198883 

Polo Version 0.1.0

Polo Version 0.1.0

Main Updates

• General bug fixes
• Updated FTP browser back end
• Updated presentation exporter functions
• Added open recent files function
• Updated documentation website and links to HWI hosted page

Installation Guide

Windows 10

Download the Windows installer and double click to run it. Windows will likely tell you Polo is an unrecognized program. To continue with the installation click More Info and then Run Anyway.

Mac OS >= High Sierra and Ubuntu >= 20.04.1 LTS x86_64

Download the Polo version for your OS and un-compress the file. You can then run the program by double clicking or with the command ./Polo.exe. Make sure you allow execution of Polo as a program.

If you run into any issues, more information can be found at the Polo website install guide page.

All versions of the program may take up to a minute to launch depending on your computer specs.

Test Data

If you do not have your own screening images you can download test images from the test data release page.

For More Information …

Visit the Polo documentation website for guides, video tutorials and troubleshooting help.

Post Release Updates

09/27/2020

• Fix shortcuts for pop out image viewer and slideshow viewer
• Grammatical fixes on a few buttons
• Added md5 checksums for all releases in checklist.txt

10/11/2020

• Update Polo logo
• Fix issue with membrane screen recognition
• Update checklist.txt to reflect new files

12/8/2020

• Reduce sig figs displayed by table view
• Update Pyinstaller spec file
• Add warning if attempting to classify non-visible ( brightfield) images
• Add warning if attempting to re-classify a run

12/17/2020

• Fix issue where users could not uncheck items in the table view

test-data

Test Data for Polo

This is not a Polo release, but includes data you can test out Polo with if you do not have your own. Test data is being included as a release as the files are too large to be added to the GitHub repository directly. Images are from a lysozyme test run.

Data Details

There are 5 rar files, all of the same sample. Files which include -jpg are visible (brightfield) images, with -shg are SHG images and with -uvt are UV-TPEF images.

test_data_chk.txt contains md5 checksums for all rar files.

Updates

• Added relabeled test data for v21 screen. This is just X000015862202008181131-jpg.rar where all date information has been changed to
  4/21/23. File added is X000015862202304211131-jpg-21-test.zip