From 97b6680c370a73c8d088d957ae012a2f0a733f83 Mon Sep 17 00:00:00 2001 From: Christoph Sommer Date: Mon, 30 Oct 2023 14:57:49 +0100 Subject: [PATCH] added doc 1/n --- docs/source/index.rst | 22 ++++++++++++++++++++-- docs/source/introduction.rst | 5 ++--- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 6301ea1..5454528 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -7,15 +7,33 @@ In time-lapse imaging, a motorized microscope repeatedly captures images at spec The reasons are complex and manifold, but it typically results from error propagation in odometry, thermal expansion, and mechanical movement. Drift poses problems for subsequent image analysis and needs to be corrected. -With Napari-correct-drift provides an extensible solution with similar functionality as Fiji’s Correct-3D-drift macro. It offers efficient cross-correlation using Fourier phase correlation, improved key frame selection, and outlier handling. Users are enabled to select ROIs to effectively stabilize given regions-of-interest in up-to 3D-multi-channel images. +With Napari-correct-drift provides an extensible solution with similar functionality as Fiji’s Correct-3D-drift macro. It offers efficient cross-correlation using Fourier phase correlationmethod, improved key frame selection, and outlier handling. In Napari users can provide a regions-of-interest (ROI) to effectively stabilize objects in up-to 3D-multi-channel images. Additionally, estimated drifts can be exported, imported, or edited before applying the correction. When to use this plugin ----------------------- #. Your time-series images or volumes exhibit *translational* drift, i. e. rigid movement, without rotation. -#. Reference channel with fixed object (e. g. beads) visualizing the drift +#. Reference channel with fixed object (e. g. fiducial) visualizing the drift #. Stabilizing objects of interest by using a ROIs +Without Napari viewer +--------------------- + +Napari-Correct-Drift can also be used without starting the Napari viewer. + +.. code-block:: python + + from napari_correct_drift import CorrectDrift + + # multi-channel 2D-movie + cd = CorrectDrift(img_in, "tcyx") + + # estimate drift table + drifts = cd.estimate_drift(t0=0, channel=0) + + # correct drift + img_cor = cd.apply_drifts(drifts) + Issues and contributing ----------------------- diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst index a29229b..96a40f5 100644 --- a/docs/source/introduction.rst +++ b/docs/source/introduction.rst @@ -1,10 +1,9 @@ Introduction ============ - Example ------- -.. .. raw:: html +.. raw:: html -.. +