| --- |
| title: Hemocytometer Ground Truth |
| emoji: 🎯 |
| colorFrom: blue |
| colorTo: yellow |
| sdk: gradio |
| sdk_version: 5.35.0 |
| app_file: app.py |
| pinned: false |
| --- |
| |
| # Hemocytometer ground truth |
|
|
| Annotation tool for building ground-truth counts of the 4×4 hemocytometer block. |
| Two tabs: **Single image** and **4 squares**. |
|
|
| ## Single image |
|
|
| 1. **Upload** one photo. |
| 2. **Click the 4 corners** of the 4×4 block (any order). Drag a handle to adjust it. |
| 3. **Segment.** The block is warped to an upright square (≤1024 px) and segmented with the |
| fine-tuned hemocytometer Cellpose-SAM model. |
| 4. **Correct the count** (see below). |
|
|
| ## 4 squares |
|
|
| 1. **Upload** the four square images at once. They are sorted by filename into Square 1–4. |
| 2. **Set each block:** click its 4 corners, or press **⌖ Auto** and click the block centre |
| to auto-detect the grid. Drag any handle to adjust. |
| 3. **Segment all 4.** One GPU call per square, as in the main counter. The time from the |
| click until all four squares are ready to annotate is recorded (end-to-end), along |
| with the server's own time. |
| 4. **Correct each square** on the large canvas below. Switch squares with the buttons or |
| keys **1–4**; edits on each square are kept when you switch. |
| 5. **Copy the results row** (or **Copy with header** the first time) and paste it into a |
| spreadsheet. Columns: `timestamp, files, model_sq1, corrected_sq1, … model_sq4, |
| corrected_sq4, mean_corrected, seg_time_s, server_time_s, min_size_px`. |
| *Model* is what Cellpose counted (after min size and exclusion); *corrected* is your |
| ground truth. The table also shows the count error, (model − corrected) / corrected. |
| |
| ## Correcting the count |
| |
| - click a cell → remove it (false positive); click again → restore |
| - click empty space → add a dot (false negative) |
| - click a dot → delete it |
| - **Shift+click** → always add a dot, even on top of a cell (e.g. two cells merged into one mask) |
| - **Ctrl+Z / Ctrl+Shift+Z** undo / redo · **Space** (hold) hide outlines · **F** fit |
| - mouse wheel zooms, drag pans |
| |
| The total is the count of detected objects, minus objects below the min size, minus |
| objects touching the left or bottom 1% exclusion zones, minus removed, plus added dots. |
| |
| Everything after segmentation runs in the browser, so clicks are instant. The page |
| keeps nothing: copy the results row (or write the count down) before uploading the |
| next image. |
| |
| ## Files |
| |
| `app.py` (server), `gt_canvas.js` (annotation canvas), `corner_canvas.js` (4-corner |
| canvases in the 4-squares tab), `grid_seeded.py` (grid auto-detection, a copy of the |
| main app's), `requirements.txt`. |
|
|
| Set hardware to **ZeroGPU** in the Space settings. To use local weights instead of the |
| Hub file, set `CPCC_LOCAL_MODEL=/path/to/weights.npy`. |
|
|
