96-Well Plate Viewer

This desktop application allows you to browse image datasets from high-content microscopy (e.g., Incucyte) using a plate-based interface. Made with PyQt.

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Features

• Plate overview with clickable wells arranged in standard 96-well plate layout (8x12)
• Full-resolution zoomable view per well with timepoint toggling
• Zoom state is preserved when toggling between timepoints—focus stays on your region of interest
• Well annotation options: singlet [1] (blue box), doublet [2] (red box), inconclusive [3] (orange box)
• Colored ring indicators on plate view based on annotations
• Export annotations to CSV with plate+well and annotation type
• Keyboard shortcuts for fast navigation and annotation

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File format requirements

Each image filename must include:

• The word plate (case-insensitive) or the letter 'p', followed by a plate identifier (e.g., PLATE01)
• A well ID in the format A1–H12
• A timepoint in the format 00d00h00m

Example:

20250117_MEM1003_plate01_A7_1_12d23h59m.tif

Other filename content is allowed, but the three components above must be present.

Optional: View the GFP channel

• If you want to display a GFP overlay for a well/timepoint, include GFP (case-insensitive) somewhere in the filename for that image.
• Any image without GFP in the filename is treated as a grayscale (brightfield) image by default.
• You do not need to include "grayscale" in filenames—grayscale is assumed unless "GFP" is present.

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First time setup

1. Install Python:
   Download and install Python 3.7 or newer from python.org.

2. Open a terminal or command prompt:
   On Mac, open Terminal. On Windows, open Command Prompt.

3. Install dependencies:
   Run the following command:

   pip install PyQt5 Pillow

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Launch the app

python plateViewer.py

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Select image folder

• When prompted, select the folder containing your .tif images.
• The app could take a few seconds to load up depending on the number of plates you have.

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Browse plates

• Use the dropdown menu at the top to switch between plates.

• Click any well to open its images. (Note: well A1 is pre-cached and is fastest to start with)

Navigate timepoints

• Use the timepoint buttons above the image.

• Or use the keyboard:

  • A → Previous timepoint
  • D → Next timepoint

• Scroll to zoom in and out of areas of interest.

  Zoom state is preserved when switching timepoints.

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Navigate between wells

• Use the ← Previous and Next → buttons below the image.

• Or use the keyboard:

  • S → Previous well
  • F → Next well

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Toggle GFP overlay (if applicable)

• Use the checkbox or press W to show/hide the GFP overlay.

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Label wells

• Use the labeled checkboxes in well view:

  • 🟦 singlet → press 1
  • 🟥 doublet → press 2
  • 🟧 inconclusive → press 3

• The selected well gets annotated with a colored outline in plate view, and logged in a later downloadable .csv format.

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Export annotations

• Click Export Annotations to CSV (top bar) to save a spreadsheet of all marked wells.
• The CSV will have two columns:
  • clone (e.g., 1A1, 2C3)
  • incucyteNote (singlet, doublet, or inconclusive)

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Return to plate view

• Click Back to Plate View to go back.

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Keyboard shortcuts

Key	Action
A	Previous timepoint
D	Next timepoint
S	Previous well
F	Next well
W	Toggle GFP overlay
1	Mark as singlet (blue)
2	Mark as doublet (red)
3	Mark as inconclusive (orange)
Ctrl+E	Export annotations to CSV

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Notes for other size plates

• The app is designed for 96-well plates by default, but should work with images from other well plate sizes (it will still display a 96-well grid).

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Author

Developed by @madelinemelzer