From 765355138201f3cdd4b75a8b7695fe98d78843e7 Mon Sep 17 00:00:00 2001 From: William Moore Date: Thu, 11 Jul 2019 23:04:23 +0100 Subject: [PATCH] Fixes to README based on feedback PR #28 --- README.rst | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/README.rst b/README.rst index 8979fd51..83d48bca 100644 --- a/README.rst +++ b/README.rst @@ -7,7 +7,8 @@ OMERO metadata plugin ===================== -Plugin for use in the OMERO CLI. +Plugin for use in the OMERO CLI. Provides tools for bulk +management of annotations on objects in OMERO. Requirements ============ @@ -43,6 +44,9 @@ Help for each command can be shown using the ``-h`` flag. Objects can be specified as arguments in the format ``Class:ID``, such as ``Project:123``. +Bulk-annotations are HDF-based tables with the NSBULKANNOTATION +namespace, sometimes referred to as OMERO.tables. + Available subcommands are: - ``allanns``: Provide a list of all annotations linked to the given object @@ -52,7 +56,6 @@ Available subcommands are: - ``original``: Print the original metadata in ini format - ``pixelsize``: Set physical pixel size - ``populate``: Add metadata (bulk-annotations) to an object (see below) -- ``populateroi``: Add ROIs to an object - ``rois``: Manage ROIs - ``summary``: Provide a general summary of available metadata - ``testtables``: Tests whether tables can be created and initialized @@ -81,7 +84,7 @@ Column Types are: These can be specified in the first row of a ``CSV`` with a ``# header`` tag (see examples below). The ``# header`` row is optional. Default column type is ``String``. -NB: Column names should not contain whitespace if you want to be able to query +NB: Column names should not contain spaces if you want to be able to query by these columns. Examples: @@ -94,7 +97,7 @@ and ``Image Name``:: project.csv:: # header s,s,d,l,s - Image Name,Dataset Name,Bounding_Box,Channel_Index,Channel_Name + Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name img-01.png,dataset01,0.0469,1,DAPI img-02.png,dataset01,0.142,2,GFP img-03.png,dataset01,0.093,3,TRITC @@ -102,14 +105,14 @@ project.csv:: This will create an OMERO.table linked to the Project like this: -========== ============ ============ ============= ============ ===== -Image Name Dataset Name Bounding_Box Channel_Index Channel_Name Image -========== ============ ============ ============= ============ ===== -img-01.png dataset01 0.0469 1 DAPI 36638 -img-02.png dataset01 0.142 2 GFP 36639 -img-03.png dataset01 0.093 3 TRITC 36640 -img-04.png dataset01 0.429 4 Cy5 36641 -========== ============ ============ ============= ============ ===== +========== ============ ======== ============= ============ ===== +Image Name Dataset Name ROI_Area Channel_Index Channel_Name Image +========== ============ ======== ============= ============ ===== +img-01.png dataset01 0.0469 1 DAPI 36638 +img-02.png dataset01 0.142 2 GFP 36639 +img-03.png dataset01 0.093 3 TRITC 36640 +img-04.png dataset01 0.429 4 Cy5 36641 +========== ============ ======== ============= ============ ===== If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed.