acq4-autopatch 0.0.6

Description:

acq4autopatch 0.0.6

ACQ4-Autopatch
Automated cell patching extension for ACQ4
Installation
Install the package into your environment with e.g.
pip install acq4_autopatch

or
git clone https://github.com/sensapex/acq4-autopatch.git
conda develop acq4-autopatch

Customize the following to suit your hardware and add it to the modules: section of your ACQ4 default.cfg
file:
Autopatch:
module: 'acq4_autopatch.module.AutopatchModule'
config:
imagingDevice: 'Camera'
patchDevices:
PatchPipette1: (0, 0) # bottom-left quad
PatchPipette2: (50*mm, 0) # bottom-right quad
PatchPipette3: (0, 50*mm) # top-left quad
PatchPipette4: (50*mm, 50*mm) # top-right quad
plateCenter: (0, 0, 0)
wellPositions: [(0, 0), (50*mm, 0), (0, 50*mm), (50*mm, 50*mm)]
patchStates:
cell detect:
maxAdvanceDistancePastTarget: 1*um
seal:
autoSealTimeout: 60
pressureMode: 'auto'
cell attached:
autoBreakInDelay: 5.0
clean:
approachHeight: 3*mm
cleanSequence: [(-35e3, 1.0), (65e3, 1.5)] * 5
rinseSequence: [(-35e3, 3.0), (65e3, 15.0)]
cameraChannels:
# Use different (exposure, trigger) DAQ lines for each pipette device
PatchPipette1: ('/Dev1/port0/line0', '/Dev1/port0/line1')
PatchPipette2: ('/Dev2/port0/line0', '/Dev2/port0/line1')
PatchPipette3: ('/Dev3/port0/line0', '/Dev3/port0/line1')
PatchPipette4: ('/Dev4/port0/line0', '/Dev4/port0/line1')

Usage
Briefly:

Make sure you have an active Storage directory in the DataManager module.
Open the Camera module.

The first time through, use this to move each pipette into its home, clean and rinse positions.
In the main ACQ4 Manager window, save the home on each Manipulator.
In the main ACQ4 Manager window, save the clean and rinse on each PatchPipette.
Do any other calibration necessary.


For each pipette, open a separate TaskRunner module.

Enable the Clamp associated with this pipette.
Configure the tasks to be performed after a cell is patched.


Open the MultiPatch module. This is useful for monitoring.
Open the Autopatch module.

Press "Add Points" and add one in the Camera for every cell you'd like to patch. Repeat for each well.
Pick your acquisition protocol.
Press "Start"


Monitor status in the "Pipettes" pane or in the MultiPatch window.
Read through results or look at errors in the "Results" pane.

TODO create and then link to video explanation.
Licensing
All software copyright (c) 2019-2020 Sensapex. All rights reserved. It is offered under multiple different
licenses, depending on your needs:

A commercial license is appropriate for development of proprietary/commercial software where you do not want
to share any source code with third parties or otherwise cannot comply with the terms of the GNU GPL
version 3. To purchase a commercial license, contact our sales team.
Licensed under the GNU General Public License (GPL) version 3 is appropriate for the development of
open-source applications, provided you can comply with the terms and conditions of the GNU GPL version 3 (or
GNU GPL version 3). See GPL-3 for details.