PPR Wizard: Auto-populate PPR catalog draft

PPR export wizard now looks for and takes in IPI / single pulse control binary data from _shuffle.txt files during blank PPR catalog generation. Three columns are expected in the shuffle files, with the difference of the second column minus the first yielding IPI. The third column is a list of 0s and 1s, 0 if the single-pulse control comes before the paired pulse recording, 1 if after.

If the shuffle file has n rows, the metadata is associated with the first 2*n recordings of that slice/recordings if single-pulse control binary data is provided, or the first n recordings if no single-pulse control data.

Center of ROI now exports

Auto-exporter now attempts to populate X_Center and Y_Center columns in the summary csv if each ROI has its own row. In some exports, each ROI may not have its own ROI, in which case a column ROI_File provides the file path to the ROI dat file.

This should help with distance measurements (previously only electrode distance column was supported).

Exporter usability fixed; color themes

Most recent version of OrchZ fixes some issues with exporter’s summary CSV ROI file tracking as well as reports when only trace-type exports are selected. Now, the spreadsheet will list the last ROI file opened (if any) when no new ROI file match is found for the next ZDA file.

Also, Sumedha complained about the Green background of the application. Now, you can enjoy a new color theme every day for the next 160 days, after which the cycle will repeat. Today’s color theme is Dark Blue (as shown below). Visit OrchZ every day to see a new collectible theme!

roi-wizard

ROI Wizard is designed to assist in the automatic generation of ROI files.

The basic functionality now available is taking ROI files and splitting the ROIs in each into smaller ROIs, randomly and uniformly sampled from the original ROIs.
If an input ROI file contains n ROIs, n files will be created, each with randomly sampled ROIs from the corresponding ROI (files are named by corresponding ROI index).

Off to see the PPR Wizard

Hi all,

At Sumedha’s request and also at my own necessity, I have implemented auto-export for PPR experiment.
Non-polyfit traces are also now supported for the purpose of accommodating PPR workflows.

Clicking the PPR Wizard button will open a PPR-export guided workflow.

First, click Generate PPR Catalog. This will produce and open a spreadsheet listing all ZDA files in the data directory and you will need to fill the columns to specify measure windows and baseline windows (units of Points) for each zda file. Leave pulse2 fields blank if the recording is a single-pulse control. An example PPR catalog:

Finally, click Start Export. All settings on the vanilla export menu will be followed, albeit a new row for each pulse will be created in the export summary:

Backlog of Release notes: Aug - Sept 2024

With the expansion of the user base to include auto-exporting by Cory, Sumedha, and Cassandra, I am providing more documentation for updated functionality.

Sep 19, 2024

New OrchZ feature: progress bar and status messages, and a cancel button!

The progress bar will show the current progress toward the task during export, movie maker, or recording. It will also give a status with relevant information such as estimated number of frames, ZDA files, or seconds remaining until the task completes.

The cancel button will request the current operation to stop as soon as possible. When it cancels (may take several seconds), the Status will return to Idle and the program will be ready for a new task.

Also, moving the mouse to a corner of the screen will trigger a cancel during screen-control as always, but now it will not trigger a crash, allowing you to continue with your current session and all of its settings.

This feature can be downloaded with ‘git pull’ free of charge!

However, in the event that you do not like this feature or find an issue but need the old functionality, simply run ‘git checkout 8d63977’ to get the last version before this feature was added.

Sep 9, 2024

Another OrchZ update: preference files are now supported!

Since the GUI is getting quite extended, being able to save/load your settings from file may come in handy. Simply do so from the Preference menu in the newest version (previously, this menu did nothing).

The preference files themselves are also human-readable, meaning you can read or modify them in Notepad or another .txt file editor if you want. This is also especially useful to understand what settings are actually saved. See attached example file.

Sep 4, 2024

Here are two brief updates to OrchZ that you may find useful:

1. Trial-by-trial export is now supported. Simply enter the number of trials per recording that should be iterated through (shown below). Trial number will be indicated as part of the roi set name column.
2. MovieMaker now labels each frame with a timestamp, setting the first frame of the movie to t = 0 ms and assuming a frame rate of 2000 Hz, as in the attached movie.gif.

New feature: Export now supports standard deviation!

Aug 12, 2024

Hi all! New features for the auto exporting! I have also fixed some other unrelated bugs during testing, so please pull the new version regardless (completely free of charge!)

• Now choose whether you want your file identifiers to be zero-padded (e.g. 02_03_10roi.dat rather than 2_3_10roi.dat)
• Now select detection of electrode location roi files (e.g. 2_1_electrode.dat) which is then used to calculate each ROI’s distance to stimulation location, with a micron-to-pixel conversion factor entered into a field. This is used during summary generation and included as the “Stim_Distance” column if stim files are found
• Date parsing from subdirectory names now looks at the entire subdirectory name for any XX-XX-XX format, to use as a date identifier. If none is found, the entire subdirectory is used as identifier for the date/subdir containing that subset of the data. This cannot be disabled currently, so please let me know if this will cause problems for you (e.g. coinciding identifier issues).
• Now alerts user if they have the summary CSV open and asks you to close the file if the application is trying to write a new copy of the summary.