Commit d4853e3a authored by Andrew Cohen's avatar Andrew Cohen

readme

parent 59b31780
......@@ -3,7 +3,17 @@
i'm glad you're here. leverjs is a great tool for live cell & organelle image analysis. the goal is for the software to be a resource to the community (that's you). i'm grateful for help/feedback, and i support any efforts to make the tools more broadly useful.
<h1> KNOWN ISSUES </h1>
<h1> introduction </h1>
there are two ways to run lever -- standalone or client server. it's mostly the same code either way, but there are some key differences. both use a node.js backend, with a webgl2 rendering client. the standalone uses the http://electron.atom.io framework to combine nodejs with chromium into an executable that can be run on windows/mac or linux. the client server uses nodejs for the server, combining google's v8 javascript engine with operating system support (e.g. file system access and manipulation). the client is any webgl2 compatible browser -- currently chrome (suggested), firefox or opera. note that edge and safari are not supported yet (hopefully soon).
most functionality is available from either stand-alone or client-server. the exception is importing microscope files into the lever format, and using the scriptable visualization for movie making -- both of these are only available in the stand-alone (electron) app.
there are two main entry points as well -- experiment window and image window. experiment window lists all movies in a folder tree, and allows processing multiple movies. the stand-alone experiment viewer has an import tab that will convert any microscope file format into the lever format (any format compatible with bioformats -- see http://www.openmicroscopy.org/bio-formats/).
the image window shows the images together with analysis results, with play/pause, zoom, view control, etc. the stand-alone image window has a server tab that allows starting a client/server session and also exposes scriptable control of the viewer, including getting/setting view parameters and capturing screen shots of the rendered window to a remote client like matlab or python for scriptable movie making.
<h1> release notes </h1>
this is a preview release. this is for collaborators with Andy Cohen's (https://bioimage.coe.drexel.edu) group to have a chance to try out the new software, test features and provide feedback. a manuscript describing this work is being planned now. once that manuscript is published, the program will be released free and open source...(gpl? mit? bsd? suggestions welcome...) until then, the software is not licensed for redistribution, and is not intended for public use.
......@@ -60,7 +70,7 @@ b. the software should work on windows, unix and mac. for unix, the matlab path
for mac, i don't have a mac so it's never been tried :) but probably the hardcoded matlab path is a deal breaker...
baby steps...
<h2>debugging</h2>
<h1>debugging</h1>
0. use microsoft's visual studio code. really. it is the best option for node/electron development.
......@@ -74,11 +84,11 @@ client side javascript.
1. to debug matlab process, edit package.json and set 'noLaunchMatlab' to true. start the image window renderer program, pick your algorithms and select reseg all (or next). then start matlab. run matlabpollDB('\path\to\leverFile.LEVER'). Or, just run matlabPollDB and it usually finds the right LEVER file automagically (from lever.state tidbit left by CmdLoop.js).
<h2>scripting and image capture for visualization</h2>
<h1>scripting and image capture for visualization</h1>
see the scripting tab in the electron (stand-alone) image window for more details...
<h2>security</h2>
security is designed into leverjs at every level, from the firewall, to the nginx reverse proxy, to auth0 (link) user api tokens, to programmatic access tokens using private/public key signing. more details to follow soon...
<h1>security</h1>
security is designed into leverjs at every level, from the firewall, to the nginx reverse proxy, to auth0 (https://auth0.com) user api tokens, to programmatic access tokens using private/public key signing. more details to follow soon...
in the interim, to access the api functionality, you can use auth0 for use authentication (details TBD) or you can generate your own keys for programmatic authentication (run node.exe leverjs\keyGen.js, see matlab\+Client for examples).
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