MICC is a simple ImageJ - Macro to count cells of multiple images at once.
- ImageJ 1 (may also work on ImageJ 2)
- Download the MultiImageCellCounter.ijm (or download the whole project)
- No installation is required.
- Click on
Plugins -> Macros -> Run... - Set the desired parameters
- Click on ok
- Path to the folder containg the images.
- Please make sure only images are inside this folder.
- Minimum cell size.
- The higher, the less artifacts are detected
- Maximum cell size.
- Set to 0 if no maximum cell size is desired.
- Roundness of cell
- Fill the holes of the generated mask. This setting should not have a major impact.
- Watersheds image.
- Only turn off if the cells are very scattered.
- Excludes cells located at the edge of the image
- Select channel of image.
- Open one of the image-files.
- If several windows are opening close every window except the desired one.
- Take a look at the title. E.g.: "123-Alexa555.zvi Ch0"
- The last number is the channel.
- Set to -1 if the image has only one channel.
- If this is set, this programm will save the processed (counted) images to this folder.
Copyright (C) 2021 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0
TLDR:
| Permissions | Conditions | Limitations |
| ---------------- | ---------------------------- | ----------- |
| ✓ Commercial use | Disclose source | ✕ Liability |
| ✓ Distribution | License and copyright notice | ✕ Warranty |
| ✓ Modification | Same license | |
| ✓ Patent use | State changes | |
| ✓ Private use | | |
Go to https://github.com/not-a-feature/MultiImageCellCounter/blob/main/LICENSE to see the full version.