Skip to content, Skip to search


Cover Maker

690 bytes added, 24 January
Use HTTPS links where feasible
{{Infobox Plugin
| software = ImageJ
| name = CoverMaker
| maintainer = [ Pavel {{Person|Tomancak]}}| author = [[User:Tomancak{{Person|Pavel Tomancak]]}}, [[User:Schindelin{{Person|Johannes Schindelin]]}}| source = [{{GitHub|repo=fiji.git;a=tree;f|path=plugins/Examples/CoverMaker;hb=master in gitweb]/}}
| released = 27/05/2012
| latest version = 29/06/2012
| category = [[:Category:Plugins]]
| website =
== Introduction ==
[[Image:Haeckel embryos white.png|thumb|left|350px|'''Drawing of Haeckel embryos.''' For afficionados this is in fact Romanes' 1892 copy of the [http[wikipedia:// Ernst Haeckel|Ernst Haeckel]] drawing. If you consider Haeckel a fraud, think again and start by reading the excellent Robert J. Richards book "[ The Tragic Sense of Life]".]]
[[Image:Haeckel embryos cover.png|thumb|left|350px|'''CoverMaker rendition of Haeckel embryos''' The image was generated using a database of 66,579 images of gene expression pattern during Drosophila embryogenesis visualized by histochemical RNA in situ hybridization.<ref name="Tomancak2002">{{cite journal
Image:Bioessays_backcover.jpg|Backcover of Bioessays featuring famous drawing of early Drosophila embryogenesis by Victoria FoeImage:Methods cover 2014 small.jpg|Cover of Methods journal focused on Drosophila, edited by Nobert PerrimonImage:Bioimage Informatics cover.jpg|Cover of Bioimage Informatics 2012 conference brochureImage:NM_cover.jpg|Cover of July 2012 Issue of Nature Methods containing focus on Bioimage InformaticsImage:Cover_suggestion_5_fullres.jpg|high-resolution version of Nature Methods coverImage:Microscope_cover.png|Open clipart microscopeImage:Runt_fish_1.png|Runt expression pattern at cellular blastoderm stage of Drosophila embryogenesis Image:Cover_suggestion_1.jpg|Cover suggestion for Focus on Bioimage Informatics - logosImage:Ovary_cover_test.jpg|Stage 10 Drosophila egg chamberImage:Example_cover_embryo.png|Dorsal ectoderm expression at blastoderm satgeImage:ImageJ2_cover.jpg|ImageJ2 logoImage:Haeckel embryos cover.png|Haeckel embryosImage:Fiji cover.png|Fiji logo
== Prepare CoverMaker Database ==
In many ways preparing the image databases is a trickier business than actually performing the reconstruction. The aim of the '''''' script (Plugins -> Examples -> Cover Maker -> Prepare Cover Maker Database) is to explore your local filesystem for RGB images that could be used to build a database. As many things can go wrong in the process, it should be considered experimental.
=== Input/Search/Output ===
| Database type || scaled tiles || originals (DO NOT unzip)
| Drosophila Embryo ''in situ'' || [http 12_9.tif] (16.6MB) || [http] (1.45GB)
== Implementation and Acknowledgements ==
The plugin was written as a Jython script during the [[2011 Hackathon in Madison|Madison ImageJ2/Fiji [ hackathon] in January 2011]]. The heavy lifting is performed using [[Jython_Scripting#Inline_java_code_inside_jython:_the_Weaver|in lined]] Java code snippet courtesy of [ Albert Cardona]{{Person|Albertcardona}}. All the large scale downsampling is done using [[User:Saalfeld{{Person|Stephan Saalfeld's]] }} proper [[Downsample|downsampler]]. [[User:Schindelin{{Person|Johannes Schindelin]] }} has helped a lot with the Dialog Listeners and will maintain the plugin for posterity.
BTW, this plugin and its genesis is a great example of the power of Fiji and the hackathons. I came to the hackathon not knowing anything about python and with only basic knowledge of Java and the ImageJ code base. In ten days I had the plugin written, probably driving the Fiji geeks crazy with my constant basic (or downright stupid) questions. But the take home message for biologists is - it can be done!
Bureaucrat, emailconfirmed, incoming, administrator, uploaders