Skip to content

Commit 168d19f

Browse files
Update fast-hippos.md
1 parent af2b680 commit 168d19f

File tree

1 file changed

+7
-4
lines changed

1 file changed

+7
-4
lines changed

_pages/plugins/fast-hippos.md

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,14 +34,17 @@ Required activated [Fiji Update Sites](https://imagej.net/update-sites/following
3434
- SCF MPI CBG
3535
(- StarDist)
3636

37-
Additionally, you need a working Cellpose (2.0 or higher) environment in Python. Before running FAST-HIPPOS, make sure that the [BIOP Cellpose wrapper](https://github.com/BIOP/ijl-utilities-wrappers/blob/master/README.md#cellpose) knows where your Cellpose environment is located and which type it is (conda or venv), by filling in the top two fields in `Plugins` -> `BIOP` -> `Cellpose/Omnipose` -> `Cellpose...`:
37+
Additionally, you need a working Cellpose (2.0 or higher) environment in Python.
3838

39-
<img src="https://github.com/user-attachments/assets/fefd2857-6880-40f2-901f-c9cdc08971aa" title="BIOP Cellpose wrapper" width="600">
39+
Before running FAST-HIPPOS, make sure that the [BIOP Cellpose wrapper](https://github.com/BIOP/ijl-utilities-wrappers/blob/master/README.md#cellpose) works correctly: follow their [installation instructions](https://github.com/BIOP/ijl-utilities-wrappers/blob/master/README.md#i-installation). Then make sure that the wrapper knows where your Cellpose environment is located and which type it is (conda or venv), by filling in the top two fields in `Plugins` -> `BIOP` -> `Cellpose/Omnipose` -> `Cellpose...`:
4040

41+
<img src="https://github.com/user-attachments/assets/fefd2857-6880-40f2-901f-c9cdc08971aa" title="BIOP Cellpose wrapper" width="500">
42+
43+
You will find the FAST-HIPPOS commands in the Fiji menu under `Plugins` -> `Macros`. Below follows a description of the main command: FAST-HIPPOS. Details on the other commands follow below.
4144
<hr>
4245

43-
## Workflow
44-
1. *[Loading input images](https://github.com/Jalink-lab/dynamic-pooled-screening/#1-input-images)*
46+
## FAST-HIPPOS Workflow
47+
1. *[Input images](https://github.com/Jalink-lab/dynamic-pooled-screening/#1-input-images)*
4548
2. *[Pre-processing](https://github.com/Jalink-lab/dynamic-pooled-screening/#2-pre-processing)*
4649
3. *[Cell segmentation](https://github.com/Jalink-lab/dynamic-pooled-screening/#3-cell-segmentation)*
4750
4. *[Measuring single-cell (FLIM/intensity) traces](https://github.com/Jalink-lab/dynamic-pooled-screening/#4-measuring-single-cell-flimintensity-traces)*

0 commit comments

Comments
 (0)