From f7be1141ade237aa3f1dd097454f9dea6ff8b589 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jord=C3=A3o=20Bragantini?= Date: Thu, 2 Feb 2023 16:04:46 -0800 Subject: [PATCH 1/3] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 6fedb93..7393c7e 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,7 @@ This napari plugin allows the estimation o cell fates from incomplete tracking d Video example below: - +https://user-images.githubusercontent.com/21022743/216478216-89c1c35f-2ce4-44e8-adb8-9aeea75b5833.mp4 TODO: add to pypi From cc445f642f2da43766525e477cc9626f9d95829d Mon Sep 17 00:00:00 2001 From: Jordao Bragantini Date: Thu, 9 Feb 2023 11:32:58 -0800 Subject: [PATCH 2/3] improved description and added file format section --- README.md | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 6fedb93..2ad6bc1 100644 --- a/README.md +++ b/README.md @@ -10,26 +10,38 @@ Interactive in silico fate mapping from tracking data. -This napari plugin allows the estimation o cell fates from incomplete tracking data by building a radial regression model per time point. The user can interrogate different starting (ending) positions using a `Points` layer; the application will advent the probed coordinates forward (backward) in time, showing the estimated fate. +This napari plugin estimates the cell fates from tracking data by building a radial regression model per time point. The user can select an area of interest using a `Points` layer; the algorithm will advent the probed coordinates forward (or backward) in time, showing the estimated fate. Video example below: -TODO: add to pypi - ## Installation +TODO: add to pypi + You can install `in-silico-fate-mapping` via [pip]: pip install in-silico-fate-mapping -To install latest development version : +To install the latest development version : pip install git+https://github.com/royerlab/in-silico-fate-mapping.git + +## IO file format + +This does not depend on the file format, the only requirement is using a `Track` layer from napari. + +Despite this, we ship a reader and writer interface. It supports `.csv` files with the following reader `TrackID, t, (z), y, x`, `z` is optional. +Such that each tracklet has a unique `TrackID` and it's composed of a sequence o time and spatial coordinates. + +This is extremely similar to how napari store tracks, more information can be found [here](https://napari.org/stable/howtos/layers/tracks.html). + +Divisions are not supported at the moment. + ## Citing If used please cite: From 5fe0f445d74c705d0777a45fbcdb660da3f4446b Mon Sep 17 00:00:00 2001 From: Jordao Bragantini Date: Thu, 9 Feb 2023 11:35:28 -0800 Subject: [PATCH 3/3] minor improve file format description --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8e068dc..b6b45a8 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ To install the latest development version : ## IO file format -This does not depend on the file format, the only requirement is using a `Track` layer from napari. +This plugin does not depend on a specific file format, the only requirement is using a `Track` layer from napari. Despite this, we ship a reader and writer interface. It supports `.csv` files with the following reader `TrackID, t, (z), y, x`, `z` is optional. Such that each tracklet has a unique `TrackID` and it's composed of a sequence o time and spatial coordinates.