Commit 1f97b9e3 authored by Martin Schorb's avatar Martin Schorb
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doc

parent 96cb517d
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- render server up and running [EMBL Render server](http://render.embl.de)
- render client scripts from the compiled (mvn) [main repo](https://github.com/saalfeldlab/render): `/g/emcf/software/render/render-ws-java-client/src/main/scripts`
- render-python-apps `renderapi` from [Allen Institute](https://github.com/AllenInstitute/render-python-apps)
- render client scripts (`geometric-descriptor`) from the compiled (mvn) [main repo](https://github.com/saalfeldlab/render): `/g/emcf/software/render/render-ws-java-client/src/main/scripts`
- render-python `renderapi` (`develop`) from [Allen Institute](https://github.com/AllenInstitute/render-python-apps)
# EMBL custom Render-Python module:
......@@ -43,9 +43,3 @@ Need an additional step to create proper BDV-N5 metadata context using [PyBDV](h
# Naming conventions:
I would suggest to user the `owner` field for project types (FIB-SEM, SBEM, ...) and the `project` to describe the individual datasets. Check [this](https://github.com/saalfeldlab/render/issues/106) for how they do it at Janelia.
# Problems:
Mac: scripts:
- brew install coreutils (for greadlines)
- install JDK with install script
......@@ -4,16 +4,16 @@
The Basic installation requires the following software:
- the [Render web services](https://github.com/saalfeldlab/render) including the underlying [MongoDB](https://www.mongodb.com/) database.
- the [Render web services](https://github.com/saalfeldlab/render) including the underlying [MongoDB](https://www.mongodb.com/) database. For full functionality, it is necessary to use the current `geometric-descriptor` branch.
- render client scripts from the compiled (mvn) [main repo](https://github.com/saalfeldlab/render): These need to be accessible for all machines that run clients.
- render client scripts from the compiled (mvn) [main repo](https://github.com/saalfeldlab/render): These need to be accessible for all machines that run clients. For full functionality, it is necessary to use the current `geometric-descriptor` branch.
- render-python-apps `renderapi` from [Allen Institute](https://github.com/AllenInstitute/render-python-apps)
- render-python `renderapi` forked from [Allen Institute](https://github.com/martinschorb/render-python). This is consistent with the original `develop` branch.
- the EMBL custom Render-Python module (based on `render-modules` development at the Allen Institute). This includes the `BigFeta` global solver.
Repo: [https://github.com/martinschorb/render-modules](https://github.com/martinschorb/render-modules)
- in addition, an additional step to create proper BDV-N5 metadata context (last step `finalize`) is necessary using [PyBDV](https://github.com/constantinpape/pybdv).
- an additional step to create proper BDV-N5 metadata context (last step `finalize`) is necessary using [PyBDV](https://github.com/constantinpape/pybdv).
## Frontend
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[Here](x2go.md) you can find details on how to set up this procedure.
## How to use it
Find out how to use it [here](usage.md).
!!! caution
Do not use spaces or hash signs in the directory name
# Volume image alignment with Render
This document explains the usage of the Web UI to rund volume EM alignment workflows using the ["Render"](https://github.com/saalfeldlab/render) infrastructure.
The design of the main window, where you control and run the alignment workflow is inspired by [IMOD's](https://bio3d.colorado.edu/imod/) [`etomo`](https://bio3d.colorado.edu/imod/doc/etomoTutorial.html) main window showing the sequential main steps of the procedure in the menu column on the left and all important parameter settings belonging to the current active steps in the main page.
### caution ###
Do not use spaces or hash signs in the directory name
![startpage](img/webui_start.png "VolumeAlign WebUI startpage")
At the bottom of each page, you will find a button to start the current task (that is disabled if information is missing). Below this button, you can select which compute resource you want to use (clicking the triangle expands the selection) and the status of the current run. Below is an expandable text box which displays the log file of the current processing run.
![status](img/webui_status.png "VolumeAlign WebUI processing status")
## Data import - convert
The initial step in the alignment of volume data is to import it into Render and convert the metadata and if necessary also the image data accordingly.
......@@ -16,13 +26,18 @@ This page contains the following elements:
- The type-dependent import content (see below)
- **select Render Project** and **select Render stack:** Provide a Render project and stack name into which the metadata will be imported. **Create new Project** and **Create new Stack** define the names of new instances.
- **select target Stack:** select **Project** and **Stack:** Provide a Render project and stack name into which the metadata will be imported. **Create new Project** and **Create new Stack** define the names of new instances.
### SBEMImage
- **dataset root directory:** the directory path of the SBEMImage root directory. This is the one that contains the `tiles`, `overviews`, `workspace` and `meta` subfolders.
- **browse:** use this dropdown to browse the directory. To move up (`..`) multiple times, you have to close the selector (`x` on the very right) for each additional step up.
### SerialEM Montage
- **dataset metadata file:** the path of the `idoc` file for the SerialEM (Super)Montage.
- **browse:** use this dropdown to browse the directory. To move up (`..`) multiple times, you have to close the selector (`x` on the very right) for each additional step up.
## Generate Tile Pairs
This step will tell Render which of the tiles are neighbours in `x` and `y` and also in `z`. It will then have a collection of pairs that it can try to match with each other all in parallel.
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