From cc5c65eb4f3e811dd5147719ababf2bc8a3f7023 Mon Sep 17 00:00:00 2001 From: veegalinova Date: Thu, 8 Feb 2024 14:20:39 +0100 Subject: [PATCH] add crop instruction --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 095a33f..9c56312 100644 --- a/README.md +++ b/README.md @@ -115,8 +115,8 @@ Crop the empty background:
-2. Press `Edit › Selection › Select Bounding Box` to select the non-empty region -3. Press `Image › Crop` to crop the region +2. Press `Edit › Selection › Select Bounding Box` to select the non-empty region. If it did not work, try using `Select Bounding Box (guess background color)` +3. Press `Image › Crop` to crop the region. 4. You can scale the image to reduce its size for faster pipeline performance. Press `Image > Scale...` and enter the desired scale, like 0.5 or 0.25. @@ -162,7 +162,7 @@ To link cells between images we will be using a plugin designed for tracking - [ 3. Open up TrackMate `Plugins > Tracking > TrackMate` 4. In the first window, it's possible select out the region you want to process and click `Refresh ROI ` 5. In the next step, select the `Cellpose Detector` -6. Check if `Path to cellpose` is correct. It should be the same location that you installed your cellpose into. It should look like this: `/Users/emilianagiacomello/miniforge3/envs/cellpose/bin/python` +6. Check if `Path to cellpose` is correct. It should be the same location that you installed your cellpose into. It should look like: `/Users/emilianagiacomello/miniforge3/envs/cellpose/bin/python` 7. Select `Custom` model from `Pretrained model` and add a path to the downloaded model. 8. Check if the approximate diameter of your objects in `Cell diameter` is correct. Here is an example of final settings: