NeuroPAL Auto-ID Software v1.8

This software performs semi-automated detection and identification of neurons in NeuroPAL image volumes.

Compiled software and manuals are now available from:
https://www.yeminilab.org/neuropal/

Please see the the NeuroPAL publication for further details:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2

The free preprint is available here:
https://www.biorxiv.org/content/10.1101/676312v2

Release notes:

1. The software and info have now migrated to www.yeminilab.org
2. Fixed minor bugs related to switching between neural atlases and unselecting neurons.

NeuroPAL Auto-ID Software v1.7

This software performs semi-automated detection and identification of neurons in NeuroPAL image volumes.

Please see the the NeuroPAL publication for further details:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2

Compiled software is available from:
https://www.hobertlab.org/neuropal/

Compiled software will soon transfer to:
https://www.yeminilab.com/software/

Release notes:

1. Updated GFP intensity estimation for image analysis.

NeuroPAL Auto-ID Software v1.6

This software performs semi-automated detection and identification of neurons in NeuroPAL image volumes.

Please see the the NeuroPAL publication for further details:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2

Compiled software is available from:
https://www.hobertlab.org/neuropal/

Compiled software will soon transfer to:
https://www.yeminilab.com/software/

Release notes:

1. Fixed a bug in the color atlas overlay.
2. Started the software migration to www.yeminilab.com

NeuroPAL Auto-ID Software v1.5

This software performs semi-automated detection and identification of neurons in NeuroPAL image volumes.

Please see the the NeuroPAL publication for further details:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2

Compiled software is available from:
https://www.hobertlab.org/neuropal/

Compiled software will soon transfer to:
https://www.yeminilab.com/software/

Release notes:

1. Added neural network (NN) detection of neurons in images (credit: Amin Nejatbakhsh, Paninski Lab). This detects most neurons and puts the dots right in the center. It improves upon matching pursuit (MP) detection. To use this, choose the menu “Neurons" and the menu item "Use NN-Detect Neurons”. Then use the "Auto-Detect" button to detect neurons.

2. Individual gamma adjustments are now available for each color channel (credit: Matt Creamer, Leifer Lab). For example, one can pump the panneuronal up individually if it's weak (by lowering the value of the channel's gamma). Use the "Image" menu to select these options.

3. Auto-generated PDFs have been improved (credit: Eviatar Yemini, Yemini Lab). By default, the software now circles all neurons with their color and panneuronals with grey, so that they can be easily spotted. The circles can be turned off if the user doesn't want them. Use the "Analysis" menu and the menu item "Save ID Image" to select these options.

4. Neurons can be emphasized (credit: Eviatar Yemini, Yemini Lab), for example to highlight mutations that led to duplicates. These will then be shown in PDFs and stored in outputted spreadsheets. To emphasize a neuron add “!” at the end of its name. For example, to emphasize a duplication of 2 PHCLs, label them both “PHCL!”. This aids quantification and analysis. Use the "Analysis" menu to select these options.

5. Neuron markers can be labeled as “artifact” or “mutation” to highlight these in the PDFs (credit: Amin Nejatbakhsh, Paninski Lab and Eviatar Yemini, Yemini Lab). Use the "Analysis" menu and the menu item "Save ID Image" to select these options.

6. Worms images can now be rotated by 90 degrees (credit: Amin Nejatbakhsh, Paninski Lab and Eviatar Yemini, Yemini Lab). So if the worm points up or down, the user can now make them point sideways. Worm images can also be mirrored in Z. Use the "Image" menu to select these options.

7. Images can be toggled to zoom in on vertical halves, thirds, quarters of the worm using the "h", "j", "k" keyboard shortcuts (credit: Eviatar Yemini, Yemini Lab). This can be useful when one has a head and a tail in an image.

8. Male-specific neurons are now available when labeling a worm as an "Adult" "XO" (credit: Eviatar Yemini, Yemini Lab).

9. Added neuron birth times as a reference when ID’ing younger worms (credit: Eviatar Yemini, Yemini Lab). These can be toggled by pressing “B” or through the "Display" menu.

Acknowledgments: members of the Hobert Lab helped beta test this latest version.

NeuroPAL Auto-ID Software

This software performs semi-automated detection and identification of neurons in NeuroPAL image volumes.

Please see the the NeuroPAL publication for further details:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2